| Date | Panel | Item | Activity | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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| Skeletal dysplasia v2.206 | KDELR2 | Arina Puzriakova Phenotypes for gene: KDELR2 were changed from Increased susceptibility to fractures; joint hypermobility; Scoliosis; Bowing of the legs; Bowing of the arms; Osteogenesis imperfecta to Osteogenesis imperfecta, type XXI, OMIM:619131; Increased susceptibility to fractures; Joint hypermobility; Scoliosis; Bowing of the legs and arms | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Skeletal dysplasia v2.205 | COL1A2 | Eleanor Williams Phenotypes for gene: COL1A2 were changed from Ehlers-Danlos syndrome, cardiac valvular form 225320; Ehlers-Danlos syndrome, type VIIB 130060; Osteogenesis imperfecta, type II 166210; Osteogenesis imperfecta, type III 259420; Osteogenesis imperfecta, type IV 166220 to Ehlers-Danlos syndrome, cardiac valvular form, OMIM:225320; Ehlers-Danlos syndrome, type VIIB, OMIM:130060; Osteogenesis imperfecta, type II, OMIM:166210; Osteogenesis imperfecta, type III, OMIM:259420; Osteogenesis imperfecta, type IV, OMIM:166220 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Skeletal dysplasia v2.179 | PISD | Eleanor Williams Phenotypes for gene: PISD were changed from Liberfarb syndrome, 618889 to Liberfarb syndrome, OMIM:618889 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Skeletal dysplasia v2.171 | LTBP3 |
Eleanor Williams changed review comment from: This gene originally had the mode of inheritance set to monoallelic based on the Geleophysic dysplasia 3 OMIM:617809 phenotype. As Tracy Lester reports there are more than cases of patients with both a dental phenotype and short stature and so the mode of inheritance should be updated to both mono- and bi-allelic. PMID: 25899461 - Dugan et al 2015 - 2 sisters with homozygous truncating mutations (1 bp insertion) in LTBP3. Only this gene was analysed. They presented with oligodontia, short stature and mitral valve prolapse. PMID: 25669657 - Huckert et al 2015 - report 4 families (3 consanguineous) with a phenotype of significant short stature with brachyolmia and hypoplastic amelogenesis imperfecta. WES identified homozygous or compound het protein altering variants in LTBP3 in all patients (14 bp deletion, nonsense variant, splice site variant, 2 1bp deletions). PMID:19344874 - Noor et al 2009 - consanguineous Pakistani family with oligodontia along with short stature in an autosomal-recessive fashion. A homozygous nonsense mutation, Y774X, within LTBP3 was identified. PMID: 8721563 (abstract only accessed) and PMID: 19213025 report patients with a dental and skeletal phenotype but no genetic analysis.; to: This gene originally had the mode of inheritance set to monoallelic based on the Geleophysic dysplasia 3 OMIM:617809 phenotype. This is supported by heterozygous variants in LTBP3 reported in PMID: 27068007 (McInerney-Leo et al 2016) - 2 cases with geleophysic dysplasia and 1 with acromelic dysplasia and PMID: 33082559 (Marzin et al 2021) - 2 cases with geleophysic dysplasia and 1 with acromelic dysplasia . Dental anomalies are not reported in either set of cases. As Tracy Lester reports there are more than 3 cases of patients with both a dental phenotype and short stature and so the mode of inheritance should be updated to both mono- and bi-allelic. PMID: 25899461 - Dugan et al 2015 - 2 sisters with homozygous truncating mutations (1 bp insertion) in LTBP3. Only this gene was analysed. They presented with oligodontia, short stature and mitral valve prolapse. PMID: 25669657 - Huckert et al 2015 - report 4 families (3 consanguineous) with a phenotype of significant short stature with brachyolmia and hypoplastic amelogenesis imperfecta. WES identified homozygous or compound het protein altering variants in LTBP3 in all patients (14 bp deletion, nonsense variant, splice site variant, 2 1bp deletions). PMID:19344874 - Noor et al 2009 - consanguineous Pakistani family with oligodontia along with short stature in an autosomal-recessive fashion. A homozygous nonsense mutation, Y774X, within LTBP3 was identified. PMID: 8721563 (abstract only accessed) and PMID: 19213025 report patients with a dental and skeletal phenotype but no genetic analysis. |
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| Skeletal dysplasia v2.171 | LTBP3 |
Eleanor Williams edited their review of gene: LTBP3: Added comment: This gene originally had the mode of inheritance set to monoallelic based on the Geleophysic dysplasia 3 OMIM:617809 phenotype. As Tracy Lester reports there are more than cases of patients with both a dental phenotype and short stature and so the mode of inheritance should be updated to both mono- and bi-allelic. PMID: 25899461 - Dugan et al 2015 - 2 sisters with homozygous truncating mutations (1 bp insertion) in LTBP3. Only this gene was analysed. They presented with oligodontia, short stature and mitral valve prolapse. PMID: 25669657 - Huckert et al 2015 - report 4 families (3 consanguineous) with a phenotype of significant short stature with brachyolmia and hypoplastic amelogenesis imperfecta. WES identified homozygous or compound het protein altering variants in LTBP3 in all patients (14 bp deletion, nonsense variant, splice site variant, 2 1bp deletions). PMID:19344874 - Noor et al 2009 - consanguineous Pakistani family with oligodontia along with short stature in an autosomal-recessive fashion. A homozygous nonsense mutation, Y774X, within LTBP3 was identified. PMID: 8721563 (abstract only accessed) and PMID: 19213025 report patients with a dental and skeletal phenotype but no genetic analysis.; Changed mode of inheritance: BOTH monoallelic and biallelic, autosomal or pseudoautosomal |
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| Skeletal dysplasia v2.168 | DSPP |
Michael Oldridge changed review comment from: agree should be demoted to Red. Dentinogenesis imperfecta appears to only affect the teeth, no evidence of OI phenotype in these cases.; to: agree should be demoted to Red. Dentinogenesis imperfecta appears to only affect the teeth, no evidence of OI phenotype in reported cases. |
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| Skeletal dysplasia v2.168 | DSPP | Michael Oldridge reviewed gene: DSPP: Rating: RED; Mode of pathogenicity: None; Publications: ; Phenotypes: Dentinogenesis imperfecta; Mode of inheritance: None | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Skeletal dysplasia v2.126 | UNC45A | Eleanor Williams commented on gene: UNC45A: Copied this gene from the Osteogenesis imperfecta panel, as all green genes on that panel should also be green on the Skeletal dysplasia panel | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Skeletal dysplasia v2.126 | UNC45A | Eleanor Williams Entity copied from Osteogenesis imperfecta v2.37 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Skeletal dysplasia v2.125 | SGMS2 | Eleanor Williams commented on gene: SGMS2: Copied from the Osteogenesis imperfecta panel to the Skeletal dysplasia panel. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Skeletal dysplasia v2.125 | SGMS2 | Eleanor Williams Entity copied from Osteogenesis imperfecta v2.37 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Skeletal dysplasia v2.124 | DSPP | Eleanor Williams commented on gene: DSPP: This gene has been reviewed as RED on the Osteogenesis imperfecta panel by Zorntiza Stark with comment "Specifically NOT associated with fractures/OI.", and therefore has been tagged for further GMS review on this panel also. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Skeletal dysplasia v2.124 | MESD | Eleanor Williams Entity copied from Osteogenesis imperfecta v2.37 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Skeletal dysplasia v2.124 | MESD |
Eleanor Williams gene: MESD was added gene: MESD was added to Skeletal dysplasia. Sources: Expert Review Amber,Literature for-review tags were added to gene: MESD. Mode of inheritance for gene: MESD was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: MESD were set to 31564437 Phenotypes for gene: MESD were set to Osteogenesis imperfecta, type XX, OMIM:618644; Osteogenesis imperfecta, type 20, MONDO:0032846 |
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| Skeletal dysplasia v2.123 | MBTPS2 | Eleanor Williams commented on gene: MBTPS2: Copied from the Osteogenesis imperfecta panel | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Skeletal dysplasia v2.123 | MBTPS2 | Eleanor Williams Entity copied from Osteogenesis imperfecta v2.37 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Skeletal dysplasia v2.123 | MBTPS2 |
Eleanor Williams gene: MBTPS2 was added gene: MBTPS2 was added to Skeletal dysplasia. Sources: Expert list,Expert Review Amber Q3_21_rating, Q3_21_expert_review tags were added to gene: MBTPS2. Mode of inheritance for gene: MBTPS2 was set to X-LINKED: hemizygous mutation in males, biallelic mutations in females Publications for gene: MBTPS2 were set to 27380894 Phenotypes for gene: MBTPS2 were set to Osteogenesis imperfecta, type XIX, OMIM:301014; osteogenesis imperfecta, type 19, MONDO:0049223 |
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| Skeletal dysplasia v2.122 | SUCO | Eleanor Williams commented on gene: SUCO: Copied from the Osteogenesis imperfecta panel to the Skeletal Dysplasia panel. Amber rating. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Skeletal dysplasia v2.122 | SUCO | Eleanor Williams Entity copied from Osteogenesis imperfecta v2.37 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Skeletal dysplasia v2.122 | SUCO |
Eleanor Williams gene: SUCO was added gene: SUCO was added to Skeletal dysplasia. Sources: Expert Review Amber,Literature Mode of inheritance for gene: SUCO was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: SUCO were set to 29620724; 20440000 Phenotypes for gene: SUCO were set to Osteogenesis imperfecta, MONDO:0019019; skeletal dysplasia, HP:0002652; osteopenia |
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| Skeletal dysplasia v2.121 | COPB2 | Eleanor Williams Added comment: Comment on list classification: Gene copied from the Osteogenesis imperfecta panel. Leaving as amber for now, but there are 2 cases with fractures and 4 with osteopaenia, plus a mouse model with low bone mass, so sufficient to rate green after then next GMS review. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Skeletal dysplasia v2.120 | COPB2 | Eleanor Williams Entity copied from Osteogenesis imperfecta v2.36 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Skeletal dysplasia v2.118 | SPARC | Arina Puzriakova Phenotypes for gene: SPARC were changed from Osteogenesis imperfecta, type XVII 616507 to Osteogenesis imperfecta, type XVII, OMIM:616507 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Skeletal dysplasia v2.112 | WNT1 | Ivone Leong Phenotypes for gene: WNT1 were changed from {Osteoporosis, early-onset, susceptibility to, autosomal dominant}, OMIM:615221; Osteogenesis imperfecta, type XV, 615220 to {Osteoporosis, early-onset, susceptibility to, autosomal dominant}, OMIM:615221; Osteogenesis imperfecta, type XV, OMIM:615220 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Skeletal dysplasia v2.111 | WNT1 | Ivone Leong Phenotypes for gene: WNT1 were changed from osteogenesis imperfecta; OI/osteoporosis; {Osteoporosis, early-onset, susceptibility to, autosomal dominant}, 615221; Osteogenesis imperfecta, type XV, 615220 to {Osteoporosis, early-onset, susceptibility to, autosomal dominant}, OMIM:615221; Osteogenesis imperfecta, type XV, 615220 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Skeletal dysplasia v2.101 | FAM46A | Arina Puzriakova Phenotypes for gene: FAM46A were changed from Osteogenesis imperfecta, type XVIII 617952 to Osteogenesis imperfecta, type XVIII, OMIM:617952 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Skeletal dysplasia v2.78 | TMEM38B | Arina Puzriakova Phenotypes for gene: TMEM38B were changed from Osteogenesis imperfecta, type XIV 615066; Osteogenesis imperfecta, type XIV 615066; osteogenesis imperfecta; Osteogenesis imperfecta, type XIV, 615066 to Osteogenesis imperfecta, type XIV, OMIM:615066; Osteogenesis imperfecta type 14, MONDO:0014029 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Skeletal dysplasia v2.70 | NPR2 |
Eleanor Williams commented on gene: NPR2: PMID: 33288834 - Simsek-Kiper et al 2020 - they investigated 26 AMDM patients from 22 unrelated families. Sanger sequencing of NPR2 was performed in 23 patients and exome sequencing was performed in 5 patients They found NPR2 variants in 23 patients (19 were homozygotes, 4 were compound heterozygotes). 22 distinct NPR2 (NM_003995) variants (14 missense, 5 nonsense, 2 intronic, and 1 single-amino acid deletion) were detected. In 14 families, segregation analysis was performed and showed the heterozygous NPR2 carrier status of the parents. Detailed radiographic evaluations were done, showing osteopenia, shortness in long tubular bones, radial bowing and radial head dislocation in the majority of cases. Other phenotypic features included motor developmental delay (11/23), global developmental delay/intellectual disability (GDD/ID) (5/23), spinal canal stenosis (2/23), and atlantoaxial dislocation (1/23), renal abnormalities and oligodontia. However, the authors note that the high level of parental consanguinity (18 patients) might have contributed to these phenotypes, from other gene variants. The height of carrier parents was also assessed and found to be significantly lower than controls. |
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| Skeletal dysplasia v2.70 | TMEM251 |
Zornitza Stark gene: TMEM251 was added gene: TMEM251 was added to Skeletal dysplasia. Sources: Literature Mode of inheritance for gene: TMEM251 was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: TMEM251 were set to 33252156 Phenotypes for gene: TMEM251 were set to Dysostosis multiplex‐like skeletal dysplasia; severe short stature Review for gene: TMEM251 was set to AMBER Added comment: Two unrelated consanguineous families with homozygous variants (c.133C>T; p.Arg45Trp and c.215dupA; p.Tyr72Ter), with co-segregation data in one family. Preliminary in vitro functional assays conducted - Tmem251 knockdown by small interfering RNA induced dedifferentiation of rat primary chondrocytes. Sources: Literature |
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| Skeletal dysplasia v2.61 | ANO5 | Eleanor Williams Phenotypes for gene: ANO5 were changed from Gnatodiaphyseal dysplasia; Osteogenesis Imperfecta and Decreased Bone Density; skeletal dysplasias; skeletal dysplasias; Disproportionate Short Stature to Gnathodiaphyseal dysplasia OMIM:166260; gnathodiaphyseal dysplasia MONDO:0008151; Osteogenesis Imperfecta and Decreased Bone Density; skeletal dysplasias; skeletal dysplasias; Disproportionate Short Stature | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Skeletal dysplasia v2.51 | MIA3 | Eleanor Williams Phenotypes for gene: MIA3 were changed from short stature; skeletal dysplasia; amelogenesis to short stature; skeletal dysplasia; amelogenesis; dentinogenesis imperfecta; short stature; brachydactyly; Platyspondyly; insulin-dependent diabetes mellitus; sensorineural hearing loss; mild intellectual disability | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Skeletal dysplasia v2.50 | MIA3 | Eleanor Williams reviewed gene: MIA3: Rating: RED; Mode of pathogenicity: None; Publications: 32101163; Phenotypes: dentinogenesis imperfecta, short stature, brachydactyly, Platyspondyly, insulin-dependent diabetes mellitus, sensorineural hearing loss, mild intellectual disability; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Skeletal dysplasia v2.36 | MIA3 |
Aleš Maver changed review comment from: The MIA3 gene is synonymous with TANGO1 in PMID:32101163. This publication reports a synonymous substitution (NM_001324062.1:c.3621A > G) that results in functionally validated exon eight skipping, leading to a truncated TANGO1/MIA3 protein. The variant was identified in four homozygous affected sibs of a consanguineous family, that presented with severe dentinogenesis imperfecta, short stature, various skeletal abnormalities, insulin-dependent diabetes mellitus, sensorineural hearing loss, and mild intellectual disability. Functional studies in HeLa and U2OS cells revealed that the truncated TANGO1/MIA3 protein is dispersed in the ER and its expression in cells with intact endogenous TANGO1/MIA3 impairs cellular collagen I secretion (PMID:32101163). Sources: Literature; to: The MIA3 gene is synonymous with TANGO1 in PMID:32101163. This publication reports a synonymous substitution (NM_001324062.1:c.3621A > G) that results in functionally validated exon eight skipping, leading to a truncated TANGO1/MIA3 protein. The variant was identified in four homozygous affected sibs of a consanguineous family, that presented with severe dentinogenesis imperfecta, short stature, various skeletal abnormalities, insulin-dependent diabetes mellitus, sensorineural hearing loss, and mild intellectual disability. Functional studies in HeLa and U2OS cells revealed that the truncated TANGO1/MIA3 protein is dispersed in the ER and its expression in cells with intact endogenous TANGO1/MIA3 impairs cellular collagen I secretion (PMID:32101163). Sources: Literature |
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| Skeletal dysplasia v2.36 | MIA3 |
Aleš Maver changed review comment from: The MIA3 gene is synonymous with TANGO1 in PMID:32101163. This publications reports a synonymous substitution (NM_001324062.1:c.3621A > G) that results in functionally validated exon eight skipping, leading to a truncated TANGO1/MIA3 protein. The variant was identified in four homozygous affected sibs of a consanguineous family, that presented with severe dentinogenesis imperfecta, short stature, various skeletal abnormalities, insulin-dependent diabetes mellitus, sensorineural hearing loss, and mild intellectual disability. Functional studies in HeLa and U2OS cells revealed that the truncated TANGO1/MIA3 protein is dispersed in the ER and its expression in cells with intact endogenous TANGO1/MIA3 impairs cellular collagen I secretion (PMID:32101163). Sources: Literature; to: The MIA3 gene is synonymous with TANGO1 in PMID:32101163. This publication reports a synonymous substitution (NM_001324062.1:c.3621A > G) that results in functionally validated exon eight skipping, leading to a truncated TANGO1/MIA3 protein. The variant was identified in four homozygous affected sibs of a consanguineous family, that presented with severe dentinogenesis imperfecta, short stature, various skeletal abnormalities, insulin-dependent diabetes mellitus, sensorineural hearing loss, and mild intellectual disability. Functional studies in HeLa and U2OS cells revealed that the truncated TANGO1/MIA3 protein is dispersed in the ER and its expression in cells with intact endogenous TANGO1/MIA3 impairs cellular collagen I secretion (PMID:32101163). Sources: Literature |
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| Skeletal dysplasia v2.36 | MIA3 |
Aleš Maver gene: MIA3 was added gene: MIA3 was added to Skeletal dysplasia. Sources: Literature Mode of inheritance for gene: MIA3 was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: MIA3 were set to 32101163 Phenotypes for gene: MIA3 were set to short stature; skeletal dysplasia; amelogenesis Penetrance for gene: MIA3 were set to unknown Review for gene: MIA3 was set to RED Added comment: The MIA3 gene is synonymous with TANGO1 in PMID:32101163. This publications reports a synonymous substitution (NM_001324062.1:c.3621A > G) that results in functionally validated exon eight skipping, leading to a truncated TANGO1/MIA3 protein. The variant was identified in four homozygous affected sibs of a consanguineous family, that presented with severe dentinogenesis imperfecta, short stature, various skeletal abnormalities, insulin-dependent diabetes mellitus, sensorineural hearing loss, and mild intellectual disability. Functional studies in HeLa and U2OS cells revealed that the truncated TANGO1/MIA3 protein is dispersed in the ER and its expression in cells with intact endogenous TANGO1/MIA3 impairs cellular collagen I secretion (PMID:32101163). Sources: Literature |
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| Skeletal dysplasia v2.29 | KDELR2 | Eleanor Williams Phenotypes for gene: KDELR2 were changed from Increased susceptibility to fractures; joint hypermobility; Scoliosis; Bowing of the legs; Bowing of the arms to Increased susceptibility to fractures; joint hypermobility; Scoliosis; Bowing of the legs; Bowing of the arms; Osteogenesis imperfecta | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Skeletal dysplasia v2.26 | KDELR2 | Eleanor Williams edited their review of gene: KDELR2: Changed rating: GREEN; Changed publications: 33053334; Changed phenotypes: Osteogenesis imperfecta; Changed mode of inheritance: BIALLELIC, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Skeletal dysplasia v2.24 | KDELR2 |
Dmitrijs Rots gene: KDELR2 was added gene: KDELR2 was added to Skeletal dysplasia. Sources: Literature Mode of inheritance for gene: KDELR2 was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: KDELR2 were set to PMID: 33053334 Phenotypes for gene: KDELR2 were set to Increased susceptibility to fractures; joint hypermobility; Scoliosis; Bowing of the legs; Bowing of the arms Penetrance for gene: KDELR2 were set to Complete Review for gene: KDELR2 was set to GREEN Added comment: 4 families with osteogenesis imperfecta reported with functional studies reported in PMID: 33053334 Sources: Literature |
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| Skeletal dysplasia v2.12 | PISD |
Arina Puzriakova gene: PISD was added gene: PISD was added to Skeletal dysplasia. Sources: Literature for-review tags were added to gene: PISD. Mode of inheritance for gene: PISD was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: PISD were set to 31263216; 30858161; 30488656; 3561949 Phenotypes for gene: PISD were set to Liberfarb syndrome, 618889 Review for gene: PISD was set to GREEN Added comment: Associated with Liberfarb syndrome in OMIM, but not in G2P. PMID: 31263216 (2019) - In two sets of brothers from unrelated consanguineous families, sequencing revealed homozygosity for a 10-bp deletion (c.904-12_904-3delCTATCACCAC) in the PISD gene. The patients presented with Liberfarb syndrome, characterised by skeletal dysplasia, short stature, early-onset retinal degeneration, developmental delay, microcephaly, and hearing loss. Authors noted phenotypic overlap with another previously described case (PMID: 3561949 (1986)), prompting follow-up investigation using paraffin-embedded tissue which yielded an identical homozygous variant. Haplotype analysis indicated a founder effect between all five individuals. PMID: 30858161 (2019) - Two sisters with progressive short stature, skeletal dysplasia, white matter abnormalities, congenital cataracts, sensorineural hearing loss, and mild global developmental delay, associated with compound heterozygous variants (c.830G>A and c.697+5G>A) in the PISD gene. PMID: 30488656 (2019) - Two unrelated individuals with an 'unclassifiable' form of spondyloepimetaphyseal dysplasia, as well as short stature, microcephaly, mild facial dysmorphism. Vision, hearing, and psychomotor development were reported to be normal for both patients. WES identified the same homozygous missense variant (c.797G>A) in PISD in both patients. Analysis revealed a common haplotype, which indicated remote consanguinity. Supporting functional data using patient-derived fibroblasts. Sources: Literature |
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| Skeletal dysplasia v1.266 | TAPT1 | Eleanor Williams Added comment: Comment on list classification: Changing rating from red to green. Including genes that are green on the Osteogenesis imperfecta panel (panel ID:196, version 2.0) as green on the Skeletal dysplasia panel on the advice of Prof Lyn Chitty. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Skeletal dysplasia v1.264 | SPARC | Eleanor Williams Added comment: Comment on list classification: Changing rating from red to green. Including genes that are green on the Osteogenesis imperfecta panel (panel ID:196, version 2.0) as green on the Skeletal dysplasia panel on the advice of Prof Lyn Chitty. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Skeletal dysplasia v1.262 | SP7 | Eleanor Williams Added comment: Comment on list classification: Changing rating from red to green. Including genes that are green on the Osteogenesis imperfecta panel (panel ID:196, version 2.0) as green on the Skeletal dysplasia panel on the advice of Prof Lyn Chitty. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Skeletal dysplasia v1.261 | NBAS | Eleanor Williams Added comment: Comment on list classification: Changing rating from red to green. Including genes that are green on the Osteogenesis imperfecta panel (panel ID:196, version 2.0) as green on the Skeletal dysplasia panel on the advice of Prof Lyn Chitty. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Skeletal dysplasia v1.258 | FAM46A | Eleanor Williams Added comment: Comment on list classification: Changing rating from red to green. Including genes that are green on the Osteogenesis imperfecta panel (panel ID:196, version 2.0) as green on the Skeletal dysplasia panel on the advice of Prof Lyn Chitty. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Skeletal dysplasia v1.257 | FAM46A |
Eleanor Williams gene: FAM46A was added gene: FAM46A was added to Skeletal dysplasia. Sources: Other Mode of inheritance for gene: FAM46A was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: FAM46A were set to 29358272 Phenotypes for gene: FAM46A were set to Osteogenesis imperfecta, type XVIII 617952 Review for gene: FAM46A was set to GREEN Added comment: Adding gene to panel as it is green on the Osteogenesis imperfecta panel. Sources: Other |
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| Skeletal dysplasia v1.256 | CREB3L1 | Eleanor Williams changed review comment from: Comment on list classification: Changing rating from red to green. Including genes that are green on the Osteogenesis imperfecta panel (panel ID:196, version 2.0) as green on the Skeletal dysplasia panel on the advice of Lyn Chitty.; to: Comment on list classification: Changing rating from red to green. Including genes that are green on the Osteogenesis imperfecta panel (panel ID:196, version 2.0) as green on the Skeletal dysplasia panel on the advice of Prof Lyn Chitty. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Skeletal dysplasia v1.256 | DSPP | Eleanor Williams changed review comment from: Comment on list classification: Changing rating from red to green. Including genes that are green on the Osteogenesis imperfecta panel (panel ID:196, version 2.0) as green on the Skeletal dysplasia panel on the advice of Lyn Chitty.; to: Comment on list classification: Changing rating from red to green. Including genes that are green on the Osteogenesis imperfecta panel (panel ID:196, version 2.0) as green on the Skeletal dysplasia panel on the advice of Prof Lyn Chitty. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Skeletal dysplasia v1.256 | DSPP | Eleanor Williams Added comment: Comment on list classification: Changing rating from red to green. Including genes that are green on the Osteogenesis imperfecta panel (panel ID:196, version 2.0) as green on the Skeletal dysplasia panel on the advice of Lyn Chitty. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Skeletal dysplasia v1.255 | CREB3L1 | Eleanor Williams Added comment: Comment on list classification: Changing rating from red to green. Including genes that are green on the Osteogenesis imperfecta panel (panel ID:196, version 2.0) as green on the Skeletal dysplasia panel on the advice of Lyn Chitty. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Skeletal dysplasia v1.242 | SULF1 |
Eleanor Williams changed review comment from: Not associated with any phenotype in OMIM or Gene2Phenotype. PMID: 20602915 - Isidor et al 2010 - using whole-genome oligonucleotide array CGH, they identified an interstitial deletion at 8q13 in 5 patients from 4 unrelated families with Mesomelia-synostoses syndrome. The deletions vary from 582 Kb to 738 Kb in size, but invariably encompass only two genes: SULF1 and SLCO5A1. Breakpoint sequence analyses performed in two families showed nonrecurrent deletions. Codeletion of SULF1 and SLCO5A1was found in all patients, suggesting that haploinsufficiency of SULF1 combined with haploinsufficiency of SLCO5A1 (or the altered expression of a neighboring gene through position effect) could be necessary in the pathogenesis of MSS. PMID: 28328141 - Kohmoto et al 2017 - report the first Japanese case with MSS diagnosed by detecting an 8q13 deletion (581 Kb monoallelic deletion) that resulted from a unique, distant L1s‐mediated unequal NAHR event, which is different from the possible mechanisms proposed in previously reported cases. The deletion encompasses SULF1, SLCO5A1, and LINC01603. The size of the 8q13 deletion was different from those of any of the four reported deletions responsible for MSS (Isidor et al., 2010). The deletion could not be confirmed as de novo because of the unavailability of parental DNA. PMID: 30450550 - Dardis et al 2019 - describe the first patient affected by MSS without the previously described 8q13 deletions. Patient is an 8‐year‐old 46,XY male presenting the radiological and clinical hallmarks of MSS. Microdeletions of SULF1 and SLCO5A1 genes at 8q13 were absent. Sequencing of SULF1 and SLCO5A1 found 4 polymorphisms but no pathogenic mutations. However, it was found that there was monoallelic expression of SULF1 in the patient's cells, likely leading to SULF1 haploinsufficiency. There may be either a deletion of a portion of SULF1 gene not detectable by PCR or CGH array or mutations or epigenetic alterations in sequences that contribute to the regulation of SULF1 expression. Summary, there are 5 cases where deletions covering both SULF1 and SLCO5A1 are found in patients with MSS. There is one case of MSS in a patient with no detectable deletions of SULF1 and SLCO5A1, but with monoallelic expression of SULF1. There is no current regions curated by ClinGen that cover these genes.; to: Not associated with any phenotype in OMIM or Gene2Phenotype. PMID: 20602915 - Isidor et al 2010 - using whole-genome oligonucleotide array CGH, they identified an interstitial deletion at 8q13 in 5 patients from 4 unrelated families with Mesomelia-synostoses syndrome. The deletions vary from 582 Kb to 738 Kb in size, but invariably encompass only two genes: SULF1 and SLCO5A1. Breakpoint sequence analyses performed in two families showed nonrecurrent deletions. Codeletion of SULF1 and SLCO5A1was found in all patients, suggesting that haploinsufficiency of SULF1 combined with haploinsufficiency of SLCO5A1 (or the altered expression of a neighboring gene through position effect) could be necessary in the pathogenesis of MSS. PMID: 28328141 - Kohmoto et al 2017 - report the first Japanese case with MSS diagnosed by detecting an 8q13 deletion (581 Kb monoallelic deletion) that resulted from a unique, distant L1s‐mediated unequal NAHR event, which is different from the possible mechanisms proposed in previously reported cases. The deletion encompasses SULF1, SLCO5A1, and LINC01603. The size of the 8q13 deletion was different from those of any of the four reported deletions responsible for MSS (Isidor et al., 2010). The deletion could not be confirmed as de novo because of the unavailability of parental DNA. PMID: 30450550 - Dardis et al 2019 - describe the first patient affected by MSS without the previously described 8q13 deletions. Patient is an 8‐year‐old 46,XY male presenting the radiological and clinical hallmarks of MSS. Microdeletions of SULF1 and SLCO5A1 genes at 8q13 were absent. Sequencing of SULF1 and SLCO5A1 found 4 polymorphisms but no pathogenic mutations. However, it was found that there was monoallelic expression of SULF1 in the patient's cells, likely leading to SULF1 haploinsufficiency. There may be either a deletion of a portion of SULF1 gene not detectable by PCR or CGH array or mutations or epigenetic alterations in sequences that contribute to the regulation of SULF1 expression. Summary, there are 5 cases where deletions covering both SULF1 and SLCO5A1 are found in patients with MSS. There is one case of MSS in a patient with no detectable deletions of SULF1 and SLCO5A1, but with monoallelic expression of SULF1. There are no current regions curated by ClinGen that cover these genes. |
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| Skeletal dysplasia v1.220 | COG1 |
Eleanor Williams changed review comment from: Associated with Congenital disorder of glycosylation, type IIg #611209 (AR) in OMIM.; to: Associated with Congenital disorder of glycosylation, type IIg #611209 (AR) in OMIM. Clinical features include short stature, several skeletal features such as scoliosis and vertebral abnormalities. PMID: 16537452 - Foulquier et al 2006 - describe a patient with a mild form of congenital disorder of glycosylation type II with a homozygous insertion of a single nucleotide (2659-2660insC), which is predicted to lead to a premature translation stop and truncation of the C terminus of the Cog1 protein by 80 amino acids. Both parents were shown to be heterozygous for this mutation. Her skeletal features included small hands and feet, rhizomelic short stature. PMID: 19008299 - Zeevaert et al 2009 - two patients (one with consanguineous Greek-Turkish parents, the other with unrelated Bulgarian parents) with a cerebrocostomandibular-like syndrome and an intronic mutation, c.1070+5G>A, that disrupts a splice donor site and leads to skipping of exon 6, a frameshift and a premature stopcodon in exon 7. Patient 1's characteristics included multiple congenital abnormalities including Pierre-Robin sequence (cleft palate, micrognathia and glossoptosis), costovertebral anomalies including osteopenia, ribfusions and posterior rib gaps, butterfly vertebrae, misalignment of the vertebrae and a clubfoot on the right. Patient 2 presented with rhizomelic shortening of upper limbs, ulnar deviation of fingers, thoracic scoliosis, hypospadias-I and left-side cryptorchidism among other features. 3 unrelated cases. |
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| Skeletal dysplasia v1.220 | SULF1 |
Eleanor Williams commented on gene: SULF1: Not associated with any phenotype in OMIM or Gene2Phenotype. PMID: 20602915 - Isidor et al 2010 - using whole-genome oligonucleotide array CGH, they identified an interstitial deletion at 8q13 in 5 patients from 4 unrelated families with Mesomelia-synostoses syndrome. The deletions vary from 582 Kb to 738 Kb in size, but invariably encompass only two genes: SULF1 and SLCO5A1. Breakpoint sequence analyses performed in two families showed nonrecurrent deletions. Codeletion of SULF1 and SLCO5A1was found in all patients, suggesting that haploinsufficiency of SULF1 combined with haploinsufficiency of SLCO5A1 (or the altered expression of a neighboring gene through position effect) could be necessary in the pathogenesis of MSS. PMID: 28328141 - Kohmoto et al 2017 - report the first Japanese case with MSS diagnosed by detecting an 8q13 deletion (581 Kb monoallelic deletion) that resulted from a unique, distant L1s‐mediated unequal NAHR event, which is different from the possible mechanisms proposed in previously reported cases. The deletion encompasses SULF1, SLCO5A1, and LINC01603. The size of the 8q13 deletion was different from those of any of the four reported deletions responsible for MSS (Isidor et al., 2010). The deletion could not be confirmed as de novo because of the unavailability of parental DNA. PMID: 30450550 - Dardis et al 2019 - describe the first patient affected by MSS without the previously described 8q13 deletions. Patient is an 8‐year‐old 46,XY male presenting the radiological and clinical hallmarks of MSS. Microdeletions of SULF1 and SLCO5A1 genes at 8q13 were absent. Sequencing of SULF1 and SLCO5A1 found 4 polymorphisms but no pathogenic mutations. However, it was found that there was monoallelic expression of SULF1 in the patient's cells, likely leading to SULF1 haploinsufficiency. There may be either a deletion of a portion of SULF1 gene not detectable by PCR or CGH array or mutations or epigenetic alterations in sequences that contribute to the regulation of SULF1 expression. Summary, there are 5 cases where deletions covering both SULF1 and SLCO5A1 are found in patients with MSS. There is one case of MSS in a patient with no detectable deletions of SULF1 and SLCO5A1, but with monoallelic expression of SULF1. There is no current regions curated by ClinGen that cover these genes. |
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| Skeletal dysplasia v1.220 | SLCO5A1 |
Eleanor Williams commented on gene: SLCO5A1: Not associated with any phenotype in OMIM or Gene2Phenotype. PMID: 20602915 - Isidor et al 2010 - using whole-genome oligonucleotide array CGH, they identified an interstitial deletion at 8q13 in 5 patients from 4 unrelated families with Mesomelia-synostoses syndrome. The deletions vary from 582 Kb to 738 Kb in size, but invariably encompass only two genes: SULF1 and SLCO5A1. Breakpoint sequence analyses performed in two families showed nonrecurrent deletions. Codeletion of SULF1 and SLCO5A1was found in all patients, suggesting that haploinsufficiency of SULF1 combined with haploinsufficiency of SLCO5A1 (or the altered expression of a neighboring gene through position effect) could be necessary in the pathogenesis of MSS. PMID: 28328141 - Kohmoto et al 2017 - report the first Japanese case with MSS diagnosed by detecting an 8q13 deletion (581 Kb monoallelic deletion) that resulted from a unique, distant L1s‐mediated unequal NAHR event, which is different from the possible mechanisms proposed in previously reported cases. The deletion encompasses SULF1, SLCO5A1, and LINC01603. The size of the 8q13 deletion was different from those of any of the four reported deletions responsible for MSS (Isidor et al., 2010). The deletion could not be confirmed as de novo because of the unavailability of parental DNA. PMID: 30450550 - Dardis et al 2019 - describe the first patient affected by MSS without the previously described 8q13 deletions. Patient is an 8‐year‐old 46,XY male presenting the radiological and clinical hallmarks of MSS. Microdeletions of SULF1 and SLCO5A1 genes at 8q13 were absent. Sequencing of SULF1 and SLCO5A1 found 4 polymorphisms but no pathogenic mutations. However, it was found that there was monoallelic expression of SULF1 in the patient's cells, likely leading to SULF1 haploinsufficiency. There may be either a deletion of a portion of SULF1 gene not detectable by PCR or CGH array or mutations or epigenetic alterations in sequences that contribute to the regulation of SULF1 expression. Summary, there are 5 cases where deletions covering both SULF1 and SLCO5A1 are found in patients with MSS. There is one case of MSS in a patient with no detectable deletions of SULF1 and SLCO5A1, but with monoallelic expression of SULF1. There is no current regions curated by ClinGen that cover these genes. |
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| Skeletal dysplasia v1.219 | CKAP2L |
Eleanor Williams commented on gene: CKAP2L: Associated with Filippi syndrome #272440 (AR) in OMIM. Mainly a digital phenotype. PMID: 25439729 - Hussain et al 2014 - performed homozygosity mapping and whole-exome sequencing in a Sardinian family with two children with Filippi syndrome and identified a homozygous frameshift mutation, c.571dupA (p.Ile191Asnfs∗6), in CKAP2L which segregated with the disease in the family. They then sequenced CKAP2L in eight additional Filippi-syndrome-affected families (one from Italy, one from Poland, one from Turkey, and five from the UK) and identified five additional mutations in four of the further eight families affected by Filippi syndrome. Sufficient cases reported, but need to assess whether the phenotype is appropriate for the skeletal dysplasia panel. It is green on the Limb disorders panel. |
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| Skeletal dysplasia v1.198 | CREB3L1 | Eleanor Williams changed review comment from: Comment on list classification: Upgrading from red to green. Is Green on the Osteogenesis imperfecta panel and 4 cases reported.; to: Comment on list classification: Upgrading from red to green. Is Green on the Osteogenesis imperfecta panel and 4 cases reported. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Skeletal dysplasia v1.198 | DSPP | Eleanor Williams Added comment: Comment on list classification: Green on the Osteogenesis imperfecta panel so making green on this panel. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Skeletal dysplasia v1.194 | CREB3L1 | Eleanor Williams Added comment: Comment on list classification: Upgrading from red to green. Is Green on the Osteogenesis imperfecta panel and 4 cases reported. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Skeletal dysplasia v1.162 | SLC10A7 | Eleanor Williams Phenotypes for gene: SLC10A7 were changed from skeletal dysplasia and amelogenesis imperfecta to skeletal dysplasia and amelogenesis imperfecta; Short stature, amelogenesis imperfecta, and skeletal dysplasia with scoliosis 618363 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Skeletal dysplasia v1.155 | SERPINH1 |
Eleanor Williams commented on gene: SERPINH1: PMID: 20188343 - Christiansen et al 2010 - one individual with OI - identified an autosomal-recessive mutation in SERPINH1 (c.233T>C, p.Leu78Pro). PMID: 25510505 - Duran et al 2015 - two affected siblings with a moderately severe form of OI. Homozygosity for a single nucleotide variant in SERPINH1 (c.710T>C, p.237Met>Thr) was identified. The parents were carriers of the sequence change. Also Dachshund (dog) model of OI: PMID: 19629171 - Drögemüller et al 2009 - investigated Dachshunds with an autosomal recessive form of OI. A missense mutation (c.977C>T, p.L326P) located in an evolutionary conserved domain was perfectly associated with the OI phenotype. 11 affected dogs were homozygous C/C and all 13 known carriers were heterozygous C/T. Affected dogs iikely bred from a founder individual. |
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| Skeletal dysplasia v1.153 | CREB3L1 |
Eleanor Williams Added phenotypes Osteogenesis imperfecta, type XVI 616229 for gene: CREB3L1 Publications for gene CREB3L1 were changed from 25007323 to 25007323; 29936144.; 28817112 |
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| Skeletal dysplasia v1.153 | BMP1 | Eleanor Williams Added phenotypes Osteogenesis imperfecta, type XIII, 614856 for gene: BMP1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Skeletal dysplasia v1.153 | SP7 |
Eleanor Williams Added phenotypes Osteogenesis imperfecta, type XII 613849 for gene: SP7 Publications for gene SP7 were changed from 20579626 to 2057926; 29382611 |
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| Skeletal dysplasia v1.153 | P3H1 | Eleanor Williams Added phenotypes Osteogenesis imperfecta, type VIII 610915 for gene: P3H1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Skeletal dysplasia v1.153 | CRTAP | Eleanor Williams Added phenotypes Osteogenesis imperfecta, type VII 610682 for gene: CRTAP | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Skeletal dysplasia v1.153 | IFITM5 | Eleanor Williams Added phenotypes Osteogenesis imperfecta, type V 610967 for gene: IFITM5 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Skeletal dysplasia v1.153 | PPIB | Eleanor Williams Added phenotypes Osteogenesis imperfecta, type IX 259440 for gene: PPIB | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Skeletal dysplasia v1.153 | SERPINH1 |
Eleanor Williams Added phenotypes Osteogenesis Imperfecta, Recessive; OI3; Osteogenesis Imperfecta and Decreased Bone Density; skeletal dysplasias; {Preterm premature rupture of the membranes, susceptibility to}, 610504; Osteogenesis imperfecta, type X, 613848 for gene: SERPINH1 Publications for gene SERPINH1 were changed from to 25510505; 20188343 |
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| Skeletal dysplasia v1.153 | WNT1 | Eleanor Williams Added phenotypes osteogenesis imperfecta; OI/osteoporosis; {Osteoporosis, early-onset, susceptibility to, autosomal dominant}, 615221; Osteogenesis imperfecta, type XV, 615220 for gene: WNT1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Skeletal dysplasia v1.153 | SERPINF1 | Eleanor Williams Added phenotypes Osteogenesis imperfecta, type VI, 613982; osteogenesis imperfecta; OI/osteoporosis; Osteogenesis Imperfecta, Recessive for gene: SERPINF1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Skeletal dysplasia v1.153 | ALPL | Eleanor Williams Added phenotypes hypophosphatasia; skeletal dysplasias; Osteogenesis Imperfecta and Decreased Bone Density for gene: ALPL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Skeletal dysplasia v1.153 | ANO5 | Eleanor Williams Added phenotypes Gnatodiaphyseal dysplasia; Osteogenesis Imperfecta and Decreased Bone Density; skeletal dysplasias; Disproportionate Short Stature for gene: ANO5 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Skeletal dysplasia v1.153 | COL1A2 | Eleanor Williams Added phenotypes Ehlers-Danlos syndrome, cardiac valvular form 225320; Ehlers-Danlos syndrome, type VIIB 130060; Osteogenesis imperfecta, type II 166210; Osteogenesis imperfecta, type III 259420; Osteogenesis imperfecta, type IV 166220 for gene: COL1A2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Skeletal dysplasia v1.153 | ERF | Eleanor Williams Added phenotypes Chitayat syndrome - 617180; Craniosynostosis 4 600775 for gene: ERF | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Skeletal dysplasia v1.153 | SEC24D | Eleanor Williams Added phenotypes Osteogenesis Imperfecta, Cole Carpenter syndrome; Cole-Carpenter syndrome; SYNDROMIC OSTEOGENESIS IMPERFECTA for gene: SEC24D | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Skeletal dysplasia v1.153 | COL1A1 | Eleanor Williams Added phenotypes Osteogenesis imperfecta, type I 166200; Caffey disease 114000; Osteogenesis imperfecta, type III 259420; Osteogenesis imperfecta, type II 166210; Ehlers-Danlos syndrome, type VIIA 130060; Ehlers-Danlos syndrome, classic 130000; Osteogenesis imperfecta, type IV 166220 for gene: COL1A1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Skeletal dysplasia v1.153 | FKBP10 | Eleanor Williams Added phenotypes Brucks syndrome 1 - 259450; Osteogenesis imperfecta, type XI, 610968 for gene: FKBP10 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Skeletal dysplasia v1.153 | DLX3 |
Eleanor Williams Added phenotypes Amelogenesis imperfecta, type IV 104510; Trichodontoosseous syndrome 190320 for gene: DLX3 Publications for gene DLX3 were changed from 26762616; 26104267 to 26104267; 26762616 |
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| Skeletal dysplasia v1.153 | TMEM38B | Eleanor Williams Added phenotypes Osteogenesis imperfecta, type XIV 615066; Osteogenesis imperfecta, type XIV, 615066; osteogenesis imperfecta for gene: TMEM38B | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Skeletal dysplasia v1.147 | WNT1 | Tracy Lester reviewed gene: WNT1: Rating: GREEN; Mode of pathogenicity: ; Publications: ; Phenotypes: OI/osteoporosis, Osteogenesis imperfecta, type XV, 615220, {Osteoporosis, early-onset, susceptibility to, autosomal dominant}, 615221, osteogenesis imperfecta; Mode of inheritance: BOTH monoallelic and biallelic (but BIALLELIC mutations cause a more SEVERE disease form), autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Skeletal dysplasia v1.147 | TMEM38B | Tracy Lester reviewed gene: TMEM38B: Rating: GREEN; Mode of pathogenicity: ; Publications: ; Phenotypes: Osteogenesis imperfecta, type XIV 615066, Osteogenesis imperfecta, type XIV, 615066, osteogenesis imperfecta; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Skeletal dysplasia v1.147 | SP7 | Tracy Lester reviewed gene: SP7: Rating: AMBER; Mode of pathogenicity: ; Publications: 29382611, 2057926; Phenotypes: Osteogenesis imperfecta, type XII 613849; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Skeletal dysplasia v1.147 | SERPINH1 | Tracy Lester reviewed gene: SERPINH1: Rating: AMBER; Mode of pathogenicity: ; Publications: 20188343, 25510505; Phenotypes: OI3, {Preterm premature rupture of the membranes, susceptibility to}, 610504, Osteogenesis imperfecta, type X, 613848, Osteogenesis Imperfecta, Recessive, Osteogenesis Imperfecta and Decreased Bone Density, skeletal dysplasias; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Skeletal dysplasia v1.147 | SERPINF1 | Tracy Lester reviewed gene: SERPINF1: Rating: GREEN; Mode of pathogenicity: ; Publications: ; Phenotypes: OI/osteoporosis, Osteogenesis imperfecta, type VI, 613982, Osteogenesis Imperfecta, Recessive, osteogenesis imperfecta; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Skeletal dysplasia v1.147 | SEC24D | Tracy Lester reviewed gene: SEC24D: Rating: GREEN; Mode of pathogenicity: ; Publications: 25683121; Phenotypes: Cole-Carpenter syndrome, Osteogenesis Imperfecta, Cole Carpenter syndrome, SYNDROMIC OSTEOGENESIS IMPERFECTA; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Skeletal dysplasia v1.147 | PPIB | Tracy Lester reviewed gene: PPIB: Rating: GREEN; Mode of pathogenicity: ; Publications: ; Phenotypes: Osteogenesis imperfecta, type IX 259440; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Skeletal dysplasia v1.147 | P3H1 | Tracy Lester reviewed gene: P3H1: Rating: GREEN; Mode of pathogenicity: ; Publications: ; Phenotypes: Osteogenesis imperfecta, type VIII 610915; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Skeletal dysplasia v1.147 | IFITM5 | Tracy Lester reviewed gene: IFITM5: Rating: GREEN; Mode of pathogenicity: ; Publications: ; Phenotypes: Osteogenesis imperfecta, type V 610967; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Skeletal dysplasia v1.147 | FKBP10 | Tracy Lester reviewed gene: FKBP10: Rating: GREEN; Mode of pathogenicity: ; Publications: ; Phenotypes: Brucks syndrome 1 - 259450, Osteogenesis imperfecta, type XI, 610968; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Skeletal dysplasia v1.147 | ERF | Tracy Lester reviewed gene: ERF: Rating: GREEN; Mode of pathogenicity: Other - please provide details in the comments; Publications: 23354439, 26097063; Phenotypes: Craniosynostosis 4 600775, Chitayat syndrome - 617180; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted; Current diagnostic: yes | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Skeletal dysplasia v1.147 | DLX3 | Tracy Lester reviewed gene: DLX3: Rating: GREEN; Mode of pathogenicity: ; Publications: 26762616, 26104267; Phenotypes: Amelogenesis imperfecta, type IV 104510, Trichodontoosseous syndrome 190320; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Skeletal dysplasia v1.147 | CRTAP | Tracy Lester reviewed gene: CRTAP: Rating: GREEN; Mode of pathogenicity: ; Publications: ; Phenotypes: Osteogenesis imperfecta, type VII 610682; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Skeletal dysplasia v1.147 | CREB3L1 | Tracy Lester reviewed gene: CREB3L1: Rating: AMBER; Mode of pathogenicity: ; Publications: 25007323, 28817112, 29936144.; Phenotypes: Osteogenesis imperfecta, type XVI 616229; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Skeletal dysplasia v1.147 | COL1A2 | Tracy Lester reviewed gene: COL1A2: Rating: GREEN; Mode of pathogenicity: ; Publications: ; Phenotypes: Ehlers-Danlos syndrome, cardiac valvular form 225320, Ehlers-Danlos syndrome, type VIIB 130060, Osteogenesis imperfecta, type II 166210, Osteogenesis imperfecta, type III 259420, Osteogenesis imperfecta, type IV 166220; Mode of inheritance: BOTH monoallelic and biallelic, autosomal or pseudoautosomal OR MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted (if exclude 255320) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Skeletal dysplasia v1.147 | COL1A1 | Tracy Lester reviewed gene: COL1A1: Rating: GREEN; Mode of pathogenicity: ; Publications: ; Phenotypes: Caffey disease 114000, Ehlers-Danlos syndrome, classic 130000, Ehlers-Danlos syndrome, type VIIA 130060, Osteogenesis imperfecta, type I 166200, Osteogenesis imperfecta, type II 166210, Osteogenesis imperfecta, type III 259420, Osteogenesis imperfecta, type IV 166220; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Skeletal dysplasia v1.147 | BMP1 | Tracy Lester reviewed gene: BMP1: Rating: GREEN; Mode of pathogenicity: ; Publications: ; Phenotypes: Osteogenesis imperfecta, type XIII, 614856; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Skeletal dysplasia v1.147 | ANO5 | Tracy Lester reviewed gene: ANO5: Rating: GREEN; Mode of pathogenicity: ; Publications: ; Phenotypes: Gnatodiaphyseal dysplasia, Osteogenesis Imperfecta and Decreased Bone Density, skeletal dysplasias, Disproportionate Short Stature; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Skeletal dysplasia v1.147 | ALPL | Tracy Lester reviewed gene: ALPL: Rating: GREEN; Mode of pathogenicity: ; Publications: ; Phenotypes: hypophosphatasia, Osteogenesis Imperfecta and Decreased Bone Density, skeletal dysplasias; Mode of inheritance: BOTH monoallelic and biallelic (but BIALLELIC mutations cause a more SEVERE disease form), autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Skeletal dysplasia v1.146 | ERF | Eleanor Williams reviewed gene: ERF: Rating: AMBER; Mode of pathogenicity: ; Publications: ; Phenotypes: ; Mode of inheritance: | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Skeletal dysplasia v1.145 | ERF |
Eleanor Williams Source NHS GMS was added to ERF. Rating Changed from Green List (high evidence) to Green List (high evidence) |
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| Skeletal dysplasia v1.127 | SLC10A7 |
Ellen McDonagh gene: SLC10A7 was added gene: SLC10A7 was added to Unexplained skeletal dysplasia. Sources: Literature Mode of inheritance for gene: SLC10A7 was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: SLC10A7 were set to 30082715 Phenotypes for gene: SLC10A7 were set to skeletal dysplasia and amelogenesis imperfecta Added comment: PMID: 30082715 reports five different SLC10A7 variants in four patients from four unrelated families and two patients from two distantly related families. The study states that the variants segregated according to a recessive mode of inheritance, however the genotype was not shown on the pedigree diagram. Further evidence was provided in a knockout mouse model that displayed abnormal development of skeletal structures and teeth anomalies. Sources: Literature |
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| Skeletal dysplasia v1.108 | DLL4 |
Rachel Jones gene: DLL4 was added gene: DLL4 was added to Unexplained skeletal dysplasia. Sources: Other Mode of inheritance for gene: DLL4 was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Publications for gene: DLL4 were set to PMID: 26299364 Phenotypes for gene: DLL4 were set to Adams-Oliver syndrome 6 616589 Penetrance for gene: DLL4 were set to Incomplete Review for gene: DLL4 was set to GREEN Added comment: Meester et al PMID: 26299364 using candidate gene approach identified 9 heterozygous mutations in DLL4 (which is a NOTCH ligand) from 91 families - same pathway as other genes previously idetified to cause Adams Oliver syndrome. No functional studies were performed, but software predicted pathogenicity of missense mutations. Evidence of non penetrance in the paper - affected siblings inheriting mutation from seemingly unaffected parent. Sources: Other |
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