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Limb disorders v5.6 MAPKAPK5 Achchuthan Shanmugasundram Phenotypes for gene: MAPKAPK5 were changed from Developmental delay, variable brain anomalies, congenital heart defects, dysmorphism; Synpolydactyly to Neurocardiofaciodigital syndrome, OMIM:619869
Limb disorders v2.81 HEATR3 Sarah Leigh changed review comment from: Not associated with a phenotype in OMIM, Gen2Phen or MONDO. PMID: 35213692 reports five HEATR3 variants in four unrelated cases who all displayed anaemia reminiscent of Diamond-Blackfan anemia, together with bone marrow failure, short stature, facial and acromelic dysmorphic features, and intellectual disability.; to: Not associated with a phenotype in OMIM, Gen2Phen or MONDO. PMID: 35213692 reports five HEATR3 variants in four unrelated cases who all displayed anaemia reminiscent of Diamond-Blackfan anemia, together with bone marrow failure, short stature, facial and acromelic dysmorphic features, and intellectual disability. HEATR3 has been rated as Green as the affected members of 3/4 families identified had brachydactyly and other features of hands and/or feet.
Limb disorders v2.69 SMO Eleanor Williams Tag for-review was removed from gene: SMO.
Limb disorders v2.67 SMO Eleanor Williams commented on gene: SMO: The mode of inheritance of this gene has been updated following NHS Genomic Medicine Service approval.
Limb disorders v2.66 SMO Eleanor Williams Source Expert list was added to SMO.
Mode of inheritance for gene SMO was changed from MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown to BOTH monoallelic and biallelic, autosomal or pseudoautosomal
Limb disorders v2.65 SCUBE3 Sarah Leigh Phenotypes for gene: SCUBE3 were changed from Short stature, facial dysmorphism, and skeletal anomalies with or without cardiac anomalies OMIM:619184 to Short stature, facial dysmorphism, and skeletal anomalies with or without cardiac anomalies OMIM:619184; short stature, facial dysmorphism, and skeletal anomalies with or without cardiac anomalies 2 MONDO:0030953
Limb disorders v2.64 SCUBE3 Sarah Leigh gene: SCUBE3 was added
gene: SCUBE3 was added to Limb disorders. Sources: Expert Review Amber,Other
Q2_21_rating tags were added to gene: SCUBE3.
Mode of inheritance for gene: SCUBE3 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: SCUBE3 were set to 33308444
Phenotypes for gene: SCUBE3 were set to Short stature, facial dysmorphism, and skeletal anomalies with or without cardiac anomalies OMIM:619184
Penetrance for gene: SCUBE3 were set to unknown
Limb disorders v2.40 MAPKAPK5 Arina Puzriakova gene: MAPKAPK5 was added
gene: MAPKAPK5 was added to Limb disorders. Sources: Literature
Mode of inheritance for gene: MAPKAPK5 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: MAPKAPK5 were set to 33442026
Phenotypes for gene: MAPKAPK5 were set to Developmental delay, variable brain anomalies, congenital heart defects, dysmorphism; Synpolydactyly
Review for gene: MAPKAPK5 was set to AMBER
Added comment: MAPKAPK5 is not yet associated with any phenotype in OMIM (last edited on 06/04/2016) but has a 'probable' disease confidence rating for 'MAPKAPK5-associated syndrome with synpolydactyly' in Gene2Phenotype.

- PMID: 33442026 (2021) - 3 individuals from 2 families with severe developmental delay, variable brain anomalies, congenital heart defects, dysmorphic facial features, and a distinctive type of synpolydactyly with an additional hypoplastic digit between the fourth and fifth digits of hands and/or feet. Exome sequencing identified different homozygous truncating variants in MAPKAPK5 in both families, segregating with disease and unaffected parents as carriers.

Patient-derived cells showed no expression of MAPKAPK5 protein isoforms and reduced levels of the MAPKAPK5-interacting protein ERK3. F-actin recovery after latrunculin B treatment was found to be less efficient in patient-derived fibroblasts than in control cells, supporting a role of MAPKAPK5 in F-actin polymerization.

Rating Amber, awaiting further cases.
Sources: Literature
Limb disorders v2.29 SMO Eleanor Williams Tag for-review tag was added to gene: SMO.
Limb disorders v2.29 SMO Eleanor Williams Added comment: Comment on mode of inheritance: Leaving MOI has monoallelic just now, but with recommendation for updating to BOTH monoallelic and biallelic at the next review, due to additional biallelic cases now reported.
Limb disorders v2.29 SMO Eleanor Williams Mode of inheritance for gene: SMO was changed from MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Limb disorders v2.28 SMO Eleanor Williams Phenotypes for gene: SMO were changed from Polydactyly; Curry-Jones syndrome, somatic mosaic, MIM:601500; Cutaneous syndactyly; Preaxial polydactyly to Curry-Jones syndrome, somatic mosaic, OMIM:601500; postaxial polydactyly MONDO:0020927; Microcephaly HP:0000252; congenital heart disease MONDO:0005453; Hirschsprung disease MONDO:0018309
Limb disorders v2.27 SMO Eleanor Williams Publications for gene: SMO were set to 27236920
Limb disorders v2.26 SMO Eleanor Williams reviewed gene: SMO: Rating: GREEN; Mode of pathogenicity: None; Publications: 32413283; Phenotypes: postaxial polydactyly MONDO:0020927, Microcephaly HP:0000252, congenital heart disease MONDO:0005453, Hirschsprung disease MONDO:0018309; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Limb disorders v2.5 SMO Zornitza Stark reviewed gene: SMO: Rating: GREEN; Mode of pathogenicity: None; Publications: 32413283; Phenotypes: Microcephaly, congenital heart disease, polydactyly, aganglionosis; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Limb disorders v1.137 WDPCP Eleanor Williams changed review comment from: PMID: 28289185 - Bruel et al 2017 - report 1 case (patient 10) with compound heterozygous variants in WDPCP and an Oral-facial-digital syndrome phenotype which includes Post-axial polydactyly of the hands and syndactyly of the feet.

PMID: 27158779 - Toriyama et al 2016 - report 1 case of a 5-year-old male presenting with facial dysmorphism, tongue hamartoma, high arched palate, tooth abnormalities, and postaxial polydactyly. He was found to be compound heterozygous for two mutations in WDPCP, a frameshift and a missense variant predicted to alter splicing. Each parent had one of the variants. Functional studies in Xenopus MCCs and found that the frame-shift allele resulted in total loss of protein, while the point mutation led to a consistent but more modest defect in protein stability They also observed Y-shaped metacarpals and defects in tongue and palate morphology in Wdpcp mouse mutants

PMID: 25427950 - Saari et al 2015 - report 1 case of a girl with polysyndactyly, coarctation of the aorta, and tongue hamartomas. By whole exome sequencing they found she is a compound heterozygote for a frame shift mutation and a likely pathogenic sequence variant in WDPCP. The parents and two siblings were heterozygous carriers.

PMID: Kim et al 2010 - report 1 cases of a proband with a clinical diagnosis of BBS and a homozygous Fritz mutation that segregated with the disorder. Both parents and an unaffected sib were heterozygous carriers. No details

3 cases with oralfacial digitial syndrome type phenotypes and one with a clinical diagnosis of BBS.; to: PMID: 28289185 - Bruel et al 2017 - report 1 case (patient 10) with compound heterozygous variants (a missense variant and 2bp deletion leading to a frameshift) in WDPCP and an Oral-facial-digital syndrome phenotype which includes Post-axial polydactyly of the hands and syndactyly of the feet.

PMID: 27158779 - Toriyama et al 2016 - report 1 case of a 5-year-old male presenting with facial dysmorphism, tongue hamartoma, high arched palate, tooth abnormalities, and postaxial polydactyly. He was found to be compound heterozygous for two mutations in WDPCP, a frameshift and a missense variant predicted to alter splicing. Each parent had one of the variants. Functional studies in Xenopus MCCs and found that the frame-shift allele resulted in total loss of protein, while the point mutation led to a consistent but more modest defect in protein stability They also observed Y-shaped metacarpals and defects in tongue and palate morphology in Wdpcp mouse mutants

PMID: 25427950 - Saari et al 2015 - report 1 case of a girl with polysyndactyly, coarctation of the aorta, and tongue hamartomas. By whole exome sequencing they found she is a compound heterozygote for a frame shift mutation and a likely pathogenic sequence variant in WDPCP. The parents and two siblings were heterozygous carriers.

PMID: Kim et al 2010 - report 1 cases of a proband with a clinical diagnosis of BBS and a homozygous Fritz mutation that segregated with the disorder. Both parents and an unaffected sib were heterozygous carriers. No details

3 cases with oralfacial digitial syndrome type phenotypes and one with a clinical diagnosis of BBS.
Limb disorders v1.129 WDPCP Eleanor Williams commented on gene: WDPCP: PMID: 28289185 - Bruel et al 2017 - report 1 case (patient 10) with compound heterozygous variants in WDPCP and an Oral-facial-digital syndrome phenotype which includes Post-axial polydactyly of the hands and syndactyly of the feet.

PMID: 27158779 - Toriyama et al 2016 - report 1 case of a 5-year-old male presenting with facial dysmorphism, tongue hamartoma, high arched palate, tooth abnormalities, and postaxial polydactyly. He was found to be compound heterozygous for two mutations in WDPCP, a frameshift and a missense variant predicted to alter splicing. Each parent had one of the variants. Functional studies in Xenopus MCCs and found that the frame-shift allele resulted in total loss of protein, while the point mutation led to a consistent but more modest defect in protein stability They also observed Y-shaped metacarpals and defects in tongue and palate morphology in Wdpcp mouse mutants

PMID: 25427950 - Saari et al 2015 - report 1 case of a girl with polysyndactyly, coarctation of the aorta, and tongue hamartomas. By whole exome sequencing they found she is a compound heterozygote for a frame shift mutation and a likely pathogenic sequence variant in WDPCP. The parents and two siblings were heterozygous carriers.

PMID: Kim et al 2010 - report 1 cases of a proband with a clinical diagnosis of BBS and a homozygous Fritz mutation that segregated with the disorder. Both parents and an unaffected sib were heterozygous carriers. No details

3 cases with oralfacial digitial syndrome type phenotypes and one with a clinical diagnosis of BBS.
Limb disorders v1.127 SOX9 Eleanor Williams changed review comment from: Associated with Campomelic dysplasia (114290) in OMIM and CAMPOMELIC DYSPLASIA and PIERRE ROBIN SEQUENCE in Gene2Phenotype (both confirmed).

Publications relating to the duplications in the region between KCNJ2 and SOX9:

PMID: 19639023 - Kurth et al 2009 - investigated four families with symmetric brachydactyly of the hands and feet as well as hyponychia or anonychia. All affected were of normal height and had no other skeletal abnormality. They identified overlapping duplications in a ∼2 Mb interval on chromosome 17q24.3. Comparison of the four duplications revealed a minimal critical region of ∼1.2 Mb encompassing a large gene desert between KCNJ2 and SOX9. In situ hybridizations in mouse embryos, showed that Sox9 was strongly expressed in the distal mesenchymal condensations at embryonic day (E) 12.5 that will later develop into the terminal phalanges and, at a later time point (E17.5), in the anlagen of the developing claw.

PMID: 27706140 - Franke et al 2016 - used chromosome conformation capture methods to look at topologically associated domains in patient cells and mouse models where the regulatory region next to SOX9 is duplicated. They generated mice with a duplicated region associated with Cooks syndrome as reported by Kurth et al 2009 (which they call Dup-C). cHi-C of E12.5 Dup-C limb buds showed a new chromatin domain corresponding to the duplicated region.
RNA sequencing expression analysis of Dup-C limb buds at E12.5 and E17.5 confirmed the upregulation of Kcnj2, whereas other genes around the locus stayed unchanged, in particular Sox9, but also Kcnj16. Thus, the inclusion of Kcnj2 in the neo-TAD resulted in its activation by regulatory elements that originally belonged to the Sox9 TAD.


Other publications.
PMID: 21373255 - Corbani et al 2011 - reported patient with SOX9 missense mutation and mild form of campomelic dysplasia. Features include short stature, dysmorphic facial features, limitation of supination and pronation of the forearms, dysplastic nails, and bone abnormalities consisting especially of cone-shaped epiphyses of the middle phalanx of the 2nd fingers, brachydactyly and clinodactyly of the middle phalanx of both 5th fingers, short 4th metacarpals, radial and femoral head subluxation, hypoplastic scapulae, humeral and ulnar epiphyseal abnormalities, unossified symphysis pubis, and a significant delay in bone age.

PMID: 24704791 - Takenouchi et al 2014 - report patient with many features of the type 2 collagen disorder including micrognathia, cleft palate, flat midface, and visual and hearing impairment, and a retarded enchondral ossification of the appendicular skeleton during the infantile period. The patient had in addition severe developmental delay. A de novo heterozygous missense mutation, c.239T>G p.Val80Gly, in exon 1 of SOX9 was found.

Summary:
Evidence that duplication of a region upstream of SOX9 can result in a brachydactyly phenotype. This appears to be as a result of increased expression of KCNJ2. It maybe most appropriate to add this upstream region as a CNV.; to: Associated with Campomelic dysplasia (114290) in OMIM and CAMPOMELIC DYSPLASIA and PIERRE ROBIN SEQUENCE in Gene2Phenotype (both confirmed).

Publications relating to the duplications in the region between KCNJ2 and SOX9:

PMID: 19639023 - Kurth et al 2009 - investigated four families with symmetric brachydactyly of the hands and feet as well as hyponychia or anonychia. All affected were of normal height and had no other skeletal abnormality. They identified overlapping duplications in a ∼2 Mb interval on chromosome 17q24.3. Comparison of the four duplications revealed a minimal critical region of ∼1.2 Mb encompassing a large gene desert between KCNJ2 and SOX9. In situ hybridizations in mouse embryos, showed that Sox9 was strongly expressed in the distal mesenchymal condensations at embryonic day (E) 12.5 that will later develop into the terminal phalanges and, at a later time point (E17.5), in the anlagen of the developing claw.

PMID: 27706140 - Franke et al 2016 - used chromosome conformation capture methods to look at topologically associated domains in patient cells and mouse models where the regulatory region next to SOX9 is duplicated. They generated mice with a duplicated region associated with Cooks syndrome as reported by Kurth et al 2009 (which they call Dup-C). cHi-C of E12.5 Dup-C limb buds showed a new chromatin domain corresponding to the duplicated region.
RNA sequencing expression analysis of Dup-C limb buds at E12.5 and E17.5 confirmed the upregulation of Kcnj2, whereas other genes around the locus stayed unchanged, in particular Sox9, but also Kcnj16. Thus, the inclusion of Kcnj2 in the neo-TAD resulted in its activation by regulatory elements that originally belonged to the Sox9 TAD.


Other publications report SNVs and deletions of SOX9 in association with Campomelic dysplasia

Summary:
Evidence that duplication of a region upstream of SOX9 can result in a brachydactyly phenotype. This appears to be as a result of increased expression of KCNJ2. It maybe most appropriate to add this upstream region as a CNV.
Limb disorders v1.56 SOX9 Eleanor Williams commented on gene: SOX9: Associated with Campomelic dysplasia (114290) in OMIM and CAMPOMELIC DYSPLASIA and PIERRE ROBIN SEQUENCE in Gene2Phenotype (both confirmed).

Publications relating to the duplications in the region between KCNJ2 and SOX9:

PMID: 19639023 - Kurth et al 2009 - investigated four families with symmetric brachydactyly of the hands and feet as well as hyponychia or anonychia. All affected were of normal height and had no other skeletal abnormality. They identified overlapping duplications in a ∼2 Mb interval on chromosome 17q24.3. Comparison of the four duplications revealed a minimal critical region of ∼1.2 Mb encompassing a large gene desert between KCNJ2 and SOX9. In situ hybridizations in mouse embryos, showed that Sox9 was strongly expressed in the distal mesenchymal condensations at embryonic day (E) 12.5 that will later develop into the terminal phalanges and, at a later time point (E17.5), in the anlagen of the developing claw.

PMID: 27706140 - Franke et al 2016 - used chromosome conformation capture methods to look at topologically associated domains in patient cells and mouse models where the regulatory region next to SOX9 is duplicated. They generated mice with a duplicated region associated with Cooks syndrome as reported by Kurth et al 2009 (which they call Dup-C). cHi-C of E12.5 Dup-C limb buds showed a new chromatin domain corresponding to the duplicated region.
RNA sequencing expression analysis of Dup-C limb buds at E12.5 and E17.5 confirmed the upregulation of Kcnj2, whereas other genes around the locus stayed unchanged, in particular Sox9, but also Kcnj16. Thus, the inclusion of Kcnj2 in the neo-TAD resulted in its activation by regulatory elements that originally belonged to the Sox9 TAD.


Other publications.
PMID: 21373255 - Corbani et al 2011 - reported patient with SOX9 missense mutation and mild form of campomelic dysplasia. Features include short stature, dysmorphic facial features, limitation of supination and pronation of the forearms, dysplastic nails, and bone abnormalities consisting especially of cone-shaped epiphyses of the middle phalanx of the 2nd fingers, brachydactyly and clinodactyly of the middle phalanx of both 5th fingers, short 4th metacarpals, radial and femoral head subluxation, hypoplastic scapulae, humeral and ulnar epiphyseal abnormalities, unossified symphysis pubis, and a significant delay in bone age.

PMID: 24704791 - Takenouchi et al 2014 - report patient with many features of the type 2 collagen disorder including micrognathia, cleft palate, flat midface, and visual and hearing impairment, and a retarded enchondral ossification of the appendicular skeleton during the infantile period. The patient had in addition severe developmental delay. A de novo heterozygous missense mutation, c.239T>G p.Val80Gly, in exon 1 of SOX9 was found.

Summary:
Evidence that duplication of a region upstream of SOX9 can result in a brachydactyly phenotype. This appears to be as a result of increased expression of KCNJ2. It maybe most appropriate to add this upstream region as a CNV.
Limb disorders v1.39 SUFU Eleanor Williams commented on gene: SUFU: Associated with Joubert syndrome 32 (#617757) in OMIM and Joubert Syndrome with Cranio-facial and Skeletal Defects in Gene2Phenotype (probable).

PMID: 28965847 - Mori et al 2017 - 2 cases. They report four children from two unrelated consanguineous families (from Italy and Egypt) carrying homozygous missense variants (c.1217T>C,p.Ile406Thr and c.1218C>G,p.Ile406Met) in SUFU. The children presented with congenital ataxia and cerebellar vermis hypoplasia with elongated superior cerebellar peduncles (mild "molar tooth sign"), typical cranio-facial dysmorphisms (hypertelorism, depressed nasal bridge, frontal bossing), and 3 had postaxial polydactyly.
In family 1, the two affected siblings also had a homozygous missense variant in CDHR1 but is expressed only in the outer nuclear layer of the retina and pathogenic variants of this gene are known to cause an autosomal-recessive form of cone-rod dystrophy with onset in the late second decade of life (older than the probands).
Functional studies on fibroblasts and cell lines showed that the mutant proteins were less stable and more rapidly degraded than SUFU WT and had impaired ability to bind GLI3 and promote its cleavage into the repressor form GLI3R, while they maintained unaltered ability to bind GLI1. These findings suggest that both variants are hypomorphic alleles, resulting only in a partial loss of the normal gene function.
Limb disorders v1.38 TRAF7 Eleanor Williams Phenotypes for gene: TRAF7 were changed from to Cardiac, facial, and digital anomalies with developmental delay, 618164; Developmental Delay, Congenital Anomalies, and Dysmorphic Features
Limb disorders v1.37 TRAF7 Eleanor Williams changed review comment from: Associated with Cardiac, facial, and digital anomalies with developmental delay (#618164) in OMIM and Developmental Delay, Congenital Anomalies, and Dysmorphic Features in Gene2Phenotype.

PMID: 29961569 - Tokita et al. 2018 - 7 cases. They report missense variants in TRAF7 in seven unrelated individuals referred for clinical exome sequencing. There was substantial phenotypic overlap between individuals, with developmental delay, congenital heart defects, limb and digital anomalies, and dysmorphic features as key features. 6 individuals had de novo variants (absence of paternal DNA in one patient did not allow confirmation of a de novo variant), with four distinct missense changes, including a c.1964G>A (p.Arg655Gln) variant in 4 individuals. The variants affect evolutionarily conserved amino acids and are located in key functional domains.

All 7 subjects had limb and digital anomalies to a variable degree, including variant palmar/digital crease patterns (n = 6) and overlapping toes (n = 5) and clinodactyly (n=3). One subject (Subject 3) had more extensive involvement of the musculoskeletal system including scoliosis with degenerative joint disease, an asymmetric sternum, bilateral avascular necrosis of the hip, tibial malformation, valgus deformity of the ankles, flexion contractures of the hands, and subluxation of multiple joints in the hands and feet.; to: Associated with Cardiac, facial, and digital anomalies with developmental delay (#618164) in OMIM and Developmental Delay, Congenital Anomalies, and Dysmorphic Features in Gene2Phenotype.

PMID: 29961569 - Tokita et al. 2018 - 7 cases. They report missense variants in TRAF7 in seven unrelated individuals referred for clinical exome sequencing. There was substantial phenotypic overlap between individuals, with developmental delay, congenital heart defects, limb and digital anomalies, and dysmorphic features as key features. 6 individuals had de novo variants (absence of paternal DNA in one patient did not allow confirmation of a de novo variant), with four distinct missense changes, including a c.1964G>A (p.Arg655Gln) variant in 4 individuals. The variants affect evolutionarily conserved amino acids and are located in key functional domains.
All 7 subjects had limb and digital anomalies to a variable degree, including variant palmar/digital crease patterns (n = 6) and overlapping toes (n = 5) and clinodactyly (n=3). One subject (Subject 3) had more extensive involvement of the musculoskeletal system including scoliosis with degenerative joint disease, an asymmetric sternum, bilateral avascular necrosis of the hip, tibial malformation, valgus deformity of the ankles, flexion contractures of the hands, and subluxation of multiple joints in the hands and feet.
Limb disorders v1.37 TRAF7 Eleanor Williams changed review comment from: Associated with Cardiac, facial, and digital anomalies with developmental delay (#618164) in OMIM and Developmental Delay, Congenital Anomalies, and Dysmorphic Features in Gene2Phenotype.; to: Associated with Cardiac, facial, and digital anomalies with developmental delay (#618164) in OMIM and Developmental Delay, Congenital Anomalies, and Dysmorphic Features in Gene2Phenotype.

PMID: 29961569 - Tokita et al. 2018 - 7 cases. They report missense variants in TRAF7 in seven unrelated individuals referred for clinical exome sequencing. There was substantial phenotypic overlap between individuals, with developmental delay, congenital heart defects, limb and digital anomalies, and dysmorphic features as key features. 6 individuals had de novo variants (absence of paternal DNA in one patient did not allow confirmation of a de novo variant), with four distinct missense changes, including a c.1964G>A (p.Arg655Gln) variant in 4 individuals. The variants affect evolutionarily conserved amino acids and are located in key functional domains.

All 7 subjects had limb and digital anomalies to a variable degree, including variant palmar/digital crease patterns (n = 6) and overlapping toes (n = 5) and clinodactyly (n=3). One subject (Subject 3) had more extensive involvement of the musculoskeletal system including scoliosis with degenerative joint disease, an asymmetric sternum, bilateral avascular necrosis of the hip, tibial malformation, valgus deformity of the ankles, flexion contractures of the hands, and subluxation of multiple joints in the hands and feet.
Limb disorders v1.35 TRAF7 Eleanor Williams commented on gene: TRAF7: Associated with Cardiac, facial, and digital anomalies with developmental delay (#618164) in OMIM and Developmental Delay, Congenital Anomalies, and Dysmorphic Features in Gene2Phenotype.
Limb disorders v1.35 NCAPG2 Eleanor Williams changed review comment from: Associated with Khan-Khan-Katsanis syndrome (#618460) in OMIM.

PMID: 30609410 - Khan et al. 2019 - 2 unrelated cases with homozygous or compound heterozygous variants in NCAPG2.
Family 1 - female with bilateral postaxial polydactyly on the feet, moderate intellectual disability, ocular anomalies, sensorineural hearing impairment, sleep apnea, and a short stature. Renal anomalies were also observed although these resolved over time. She was found to have compound-heterozygous missense NCAPG2 mutations, c.1825A>G (p.Lys609Glu) and c.2078C>T (p.Thr693Met); three healthy siblings are either wild-type (WT) or heterozygous for the mutations (mut).
Family 2 - proband was a twin with multiple congenital anomalies at birth; these included microcephaly, facial dysmorphisms, digit abnormalities (postaxial absent toes and clinodactyly of the 5th finger), ocular phenotypes (Peters anomaly, bilateral glaucoma, and buphthalmos of the left eye), contractures, neonatal hypertonia, and a sacral dimple. A homozygous missense variant was found in the proband c.2548A>C [p.Thr850Pro]. Both parents are heterozygous for this variant.
Functional studies with skin fibroblasts from the proband in family 1, showed abnormal chromosome condensation, augmented anaphase chromatin-bridge formation, and micronuclei in daughter cells. In a ncapg2 zebrafish model, morphants displayed clinically relevant phenotypes, such as renal anomalies, microcephaly, and concomitant increases in apoptosis and altered mitotic progression. These could be rescued by wild-type but not mutant human NCAPG2 mRNA and were recapitulated in CRISPR-Cas9 F0 mutants.; to: Associated with Khan-Khan-Katsanis syndrome (#618460) in OMIM.

PMID: 30609410 - Khan et al. 2019 - 2 unrelated cases with homozygous or compound heterozygous variants in NCAPG2.
Family 1 - female with bilateral postaxial polydactyly on the feet, moderate intellectual disability, ocular anomalies, sensorineural hearing impairment, sleep apnea, and a short stature. Hydronephrosiss was also observed although this improved over time. She was found to have compound-heterozygous missense NCAPG2 mutations, c.1825A>G (p.Lys609Glu) and c.2078C>T (p.Thr693Met); three healthy siblings are either wild-type (WT) or heterozygous for the mutations (mut). Also of note was a heterozygous NPHP1 deletion, a common contributor to nephronophthisis.
Family 2 - proband was a twin with multiple congenital anomalies at birth; these included microcephaly, facial dysmorphisms, digit abnormalities (postaxial absent toes and clinodactyly of the 5th finger), ocular phenotypes (Peters anomaly, bilateral glaucoma, and buphthalmos of the left eye), contractures, neonatal hypertonia, and a sacral dimple. A homozygous missense variant was found in the proband c.2548A>C [p.Thr850Pro]. Both parents are heterozygous for this variant.
Functional studies with skin fibroblasts from the proband in family 1, showed abnormal chromosome condensation, augmented anaphase chromatin-bridge formation, and micronuclei in daughter cells. In a ncapg2 zebrafish model, morphants displayed clinically relevant phenotypes, such as renal anomalies, microcephaly, and concomitant increases in apoptosis and altered mitotic progression. These could be rescued by wild-type but not mutant human NCAPG2 mRNA and were recapitulated in CRISPR-Cas9 F0 mutants.
Limb disorders v1.35 NCAPG2 Eleanor Williams commented on gene: NCAPG2: Associated with Khan-Khan-Katsanis syndrome (#618460) in OMIM.

PMID: 30609410 - Khan et al. 2019 - 2 unrelated cases with homozygous or compound heterozygous variants in NCAPG2.
Family 1 - female with bilateral postaxial polydactyly on the feet, moderate intellectual disability, ocular anomalies, sensorineural hearing impairment, sleep apnea, and a short stature. Renal anomalies were also observed although these resolved over time. She was found to have compound-heterozygous missense NCAPG2 mutations, c.1825A>G (p.Lys609Glu) and c.2078C>T (p.Thr693Met); three healthy siblings are either wild-type (WT) or heterozygous for the mutations (mut).
Family 2 - proband was a twin with multiple congenital anomalies at birth; these included microcephaly, facial dysmorphisms, digit abnormalities (postaxial absent toes and clinodactyly of the 5th finger), ocular phenotypes (Peters anomaly, bilateral glaucoma, and buphthalmos of the left eye), contractures, neonatal hypertonia, and a sacral dimple. A homozygous missense variant was found in the proband c.2548A>C [p.Thr850Pro]. Both parents are heterozygous for this variant.
Functional studies with skin fibroblasts from the proband in family 1, showed abnormal chromosome condensation, augmented anaphase chromatin-bridge formation, and micronuclei in daughter cells. In a ncapg2 zebrafish model, morphants displayed clinically relevant phenotypes, such as renal anomalies, microcephaly, and concomitant increases in apoptosis and altered mitotic progression. These could be rescued by wild-type but not mutant human NCAPG2 mRNA and were recapitulated in CRISPR-Cas9 F0 mutants.
Limb disorders v1.30 FZD2 Eleanor Williams commented on gene: FZD2: Associated with Omodysplasia 2 (#164745) in OMIM.

Omodysplasia 2:

PMID: 25759469 - Saal et al. 2015 - 1 case - a mother and daughter with omodysplasia were found to have a FZD2 mutation (c.1644G>A, p.Trp548*). The variant was found to have occurred de novo in the mother. The altered protein is still produced in vitro, but is shown to have reduced ability to interact with its downstream target DISHEVELLED. The mother had multiple anomalies, including bilateral cleft lip and cleft palate, short upper extremities, dysmorphic facial features and hypoplastic labia and clitoris. Skeletal X rays of the daughter showed hypoplasia of T11 vertebral body and bilateral dislocation of the radius with short humeri. At 6 years musculoskeletal examination showed primarily rhizomelic shortening of the upper extremities and a mild shortening of the forearms with limited forearm supination/pronation. There was mild fifth finger clinodactyly with no brachydactyly.

Robinow syndrome:

PMID: 29276006 - White et al 2018 - 4 families with at least one individual clinical diagnosed with Robinow or Robinow-like phenotypes and with variants in FZD2 were identified . All showed limb phenotypes including mesomelic limb shortening (3 families, mild in one case), brachdactyly (3 families), proximaly implanted thumbs (1 family), Medelung deformity (1 family).
Limb disorders v0.256 SMO Rebecca Foulger Added comment: Comment on mode of inheritance: Changed MOI from 'Other' in order to capture variants within this gene in our current tiering pipeline.
Limb disorders v0.256 SMO Rebecca Foulger Mode of inheritance for gene: SMO was changed from Other to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Limb disorders v0.236 SMO Rebecca Foulger Classified gene: SMO as Green List (high evidence)
Limb disorders v0.236 SMO Rebecca Foulger Added comment: Comment on list classification: Updated rating from Red to Green: sufficient unrelated cases of syndactyly and/or preaxial polydactyly in Curry-Jones patients for inclusion on panel.
Limb disorders v0.236 SMO Rebecca Foulger Gene: smo has been classified as Green List (High Evidence).
Limb disorders v0.235 SMO Rebecca Foulger Added comment: Comment on mode of inheritance: Somatic mosaic.
Limb disorders v0.235 SMO Rebecca Foulger Mode of inheritance for gene: SMO was changed from to Other
Limb disorders v0.234 SMO Rebecca Foulger commented on gene: SMO: Added 'somatic' tag.
Limb disorders v0.234 SMO Rebecca Foulger Tag somatic tag was added to gene: SMO.
Limb disorders v0.233 TFAP2B Rebecca Foulger commented on gene: TFAP2B: Confirmed DD-G2P gene for Char syndrome (MIM:169100). Char syndrome is characterized by the triad of patent ductus arteriosus (PDA), facial dysmorphism and hand anomalies including aplasia or hypoplasia of the middle phalanges of the fifth fingers or fifth finger clinodactyly. However, hand anomalies are not reported in all patients. Variants in TFAP2B can also cause PDA without facial dysmorphism or hand anomalies (MIM:617035).
Limb disorders v0.176 SMO Rebecca Foulger commented on gene: SMO: PMID:27236920 (Twigg et al, 2016) analysed 10 unrelated patients with Curry-Jones syndrome including 6 previously reported patients. They identified somatic mosaicism for the identical L412F variant in SMO in 8 of the patients. The patients all showed cutaneous syndactyly and/or preaxial polydactyly.
Limb disorders v0.176 SMO Rebecca Foulger Phenotypes for gene: SMO were changed from Polydactyly to Polydactyly; Curry-Jones syndrome, somatic mosaic, MIM:601500; Cutaneous syndactyly; Preaxial polydactyly
Limb disorders v0.175 SMO Rebecca Foulger Publications for gene: SMO were set to
Limb disorders v0.174 SMO Rebecca Foulger Added comment: Comment on mode of pathogenicity: Somatic mosaicism.
Limb disorders v0.174 SMO Rebecca Foulger Mode of pathogenicity for gene: SMO was changed from None to Other
Limb disorders v0.173 SMO Rebecca Foulger commented on gene: SMO
Limb disorders v0.173 SMO Rebecca Foulger Tag mosaicism tag was added to gene: SMO.
Limb disorders v0.146 SMOC1 Eleanor Williams commented on gene: SMOC1
Limb disorders SMO Ellen McDonagh Added gene to panel
Limb disorders SMOC1 Ellen McDonagh classified SMOC1 as Green List (high evidence)