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| Skeletal dysplasia v9.4 | GNPNAT1 | Ida Ertmanska changed review comment from: Comment on list classification: There are now 4 unrelated individuals reported with biallelic GNPNAT1 variants and skeletal dysplasia. Hence, this gene should be promoted to Green at the next update.; to: Comment on list classification: There are now 4 unrelated individuals reported with biallelic GNPNAT1 missense variants and skeletal dysplasia. Hence, this gene should be promoted to Green at the next update. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Skeletal dysplasia v9.4 | GNPNAT1 |
Ida Ertmanska changed review comment from: PMID: 35427807 Sabbagh et al., 2022 Report of an 8yo girl with Spondyloepimetaphyseal dysplasia and a homozygous GNPNAT1 variant c.226G > A p.(Glu76Lys) - method: Trio WGS. Moroccan consanguineous parents. Language and motor development was normal. She had severe short stature due to rhizomelic shortening of the limbs. PMID: 36097642 Elhossini et al., 2022 Report of an Egyptian patient (consanguineous parents), who presented with severe Spondylo-epi-metaphyseal dysplasia. WES identified a homozygous c.77T>G, (p.Phe26Cys) variant in GNPNAT1. His main symptoms were severe short stature, rhizomelic limb shortening, and wide flared metaphysis. Short broad long bones, brachydactyly, delayed epiphyseal ossification of long bones, advanced bone age, and immunodeficiency were additional findings. In the same family, a fetus was aborted at 4 months of pregnancy due to detected skeletal deformities diagnosed intrauterine - genotype not confirmed. PMID: 39945447 Pan et al., 2025 No. 2 WES case. Ultrasound findings revealed TE, nuchal fold (NF) thickening, short limbs, and a narrow thorax, indicative of skeletal dysplasia. WES identified compound heterozygous mutations in the GNPNAT1 gene: c.305C>T/p.Thr102Ile & c.506G>T/p.Gly169Va1- both rare / absent from gnomAD v4, classified as VUS according to ACMG but reported to the family due to consistent phenotype.; to: PMID: 35427807 Sabbagh et al., 2022 Report of an 8yo girl with Spondyloepimetaphyseal dysplasia and a homozygous GNPNAT1 variant c.226G > A p.(Glu76Lys) - method: Trio WGS. Moroccan consanguineous parents. Language and motor development was normal. She had severe short stature due to rhizomelic shortening of the limbs. PMID: 36097642 Elhossini et al., 2022 Report of an Egyptian patient (consanguineous parents), who presented with severe Spondylo-epi-metaphyseal dysplasia. WES identified a homozygous c.77T>G, (p.Phe26Cys) variant in GNPNAT1. His main symptoms were severe short stature, rhizomelic limb shortening, and wide flared metaphysis. Short broad long bones, brachydactyly, delayed epiphyseal ossification of long bones, advanced bone age, and immunodeficiency were additional findings. In the same family, a fetus was aborted at 4 months of pregnancy due to detected skeletal deformities diagnosed intrauterine - genotype not confirmed. PMID: 39945447 Pan et al., 2025 No. 2 WES case. Ultrasound findings revealed TE, nuchal fold (NF) thickening, short limbs, and a narrow thorax, indicative of skeletal dysplasia. WES identified compound heterozygous mutations in the GNPNAT1 gene: c.305C>T/p.Thr102Ile & c.506G>T/p.Gly169Val- both rare / absent from gnomAD v4, classified as VUS according to ACMG but reported to the family due to consistent phenotype. |
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| Skeletal dysplasia v9.4 | GNPNAT1 | Ida Ertmanska Classified gene: GNPNAT1 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Skeletal dysplasia v9.4 | GNPNAT1 | Ida Ertmanska Added comment: Comment on list classification: There are now 4 unrelated individuals reported with biallelic GNPNAT1 variants and skeletal dysplasia. Hence, this gene should be promoted to Green at the next update. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Skeletal dysplasia v9.4 | GNPNAT1 | Ida Ertmanska Gene: gnpnat1 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Skeletal dysplasia v9.3 | GNPNAT1 | Ida Ertmanska Publications for gene: GNPNAT1 were set to 32591345 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Skeletal dysplasia v9.2 | GNPNAT1 | Ida Ertmanska Tag Q2_26_promote_green tag was added to gene: GNPNAT1. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Skeletal dysplasia v9.2 | GNPNAT1 |
Ida Ertmanska changed review comment from: PMID: 35427807 Sabbagh et al., 2022 Report of an 8yo girl with Spondyloepimetaphyseal dysplasia and a homozygous GNPNAT1 variant c.226G > A p.(Glu76Lys) - method: Trio WGS. Moroccan consanguineous parents. Language and motor development was normal. She had severe short stature due to rhizomelic shortening of the limbs. PMID: 36097642 Elhossini et al., 2022 Report of an Egyptian patient (consanguineous parents), who presented with severe Spondylo-epi-metaphyseal dysplasia. WES identified a homozygous c.77T>G, (p.Phe26Cys) variant in GNPNAT1. His main symptoms were severe short stature, rhizomelic limb shortening, and wide flared metaphysis. Short broad long bones, brachydactyly, delayed epiphyseal ossification of long bones, advanced bone age, and immunodeficiency were additional findings. PMID: 39945447 Pan et al., 2025 No. 2 WES case. Ultrasound findings revealed TE, nuchal fold (NF) thickening, short limbs, and a narrow thorax, indicative of skeletal dysplasia. WES identified compound heterozygous mutations in the GNPNAT1 gene: c.305C>T/p.Thr102Ile & c.506G>T/p.Gly169Va1- both rare / absent from gnomAD v4, classified as VUS according to ACMG but reported to the family due to consistent phenotype.; to: PMID: 35427807 Sabbagh et al., 2022 Report of an 8yo girl with Spondyloepimetaphyseal dysplasia and a homozygous GNPNAT1 variant c.226G > A p.(Glu76Lys) - method: Trio WGS. Moroccan consanguineous parents. Language and motor development was normal. She had severe short stature due to rhizomelic shortening of the limbs. PMID: 36097642 Elhossini et al., 2022 Report of an Egyptian patient (consanguineous parents), who presented with severe Spondylo-epi-metaphyseal dysplasia. WES identified a homozygous c.77T>G, (p.Phe26Cys) variant in GNPNAT1. His main symptoms were severe short stature, rhizomelic limb shortening, and wide flared metaphysis. Short broad long bones, brachydactyly, delayed epiphyseal ossification of long bones, advanced bone age, and immunodeficiency were additional findings. In the same family, a fetus was aborted at 4 months of pregnancy due to detected skeletal deformities diagnosed intrauterine - genotype not confirmed. PMID: 39945447 Pan et al., 2025 No. 2 WES case. Ultrasound findings revealed TE, nuchal fold (NF) thickening, short limbs, and a narrow thorax, indicative of skeletal dysplasia. WES identified compound heterozygous mutations in the GNPNAT1 gene: c.305C>T/p.Thr102Ile & c.506G>T/p.Gly169Va1- both rare / absent from gnomAD v4, classified as VUS according to ACMG but reported to the family due to consistent phenotype. |
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| Skeletal dysplasia v9.2 | GNPNAT1 |
Ida Ertmanska edited their review of gene: GNPNAT1: Added comment: PMID: 35427807 Sabbagh et al., 2022 Report of an 8yo girl with Spondyloepimetaphyseal dysplasia and a homozygous GNPNAT1 variant c.226G > A p.(Glu76Lys) - method: Trio WGS. Moroccan consanguineous parents. Language and motor development was normal. She had severe short stature due to rhizomelic shortening of the limbs. PMID: 36097642 Elhossini et al., 2022 Report of an Egyptian patient (consanguineous parents), who presented with severe Spondylo-epi-metaphyseal dysplasia. WES identified a homozygous c.77T>G, (p.Phe26Cys) variant in GNPNAT1. His main symptoms were severe short stature, rhizomelic limb shortening, and wide flared metaphysis. Short broad long bones, brachydactyly, delayed epiphyseal ossification of long bones, advanced bone age, and immunodeficiency were additional findings. PMID: 39945447 Pan et al., 2025 No. 2 WES case. Ultrasound findings revealed TE, nuchal fold (NF) thickening, short limbs, and a narrow thorax, indicative of skeletal dysplasia. WES identified compound heterozygous mutations in the GNPNAT1 gene: c.305C>T/p.Thr102Ile & c.506G>T/p.Gly169Va1- both rare / absent from gnomAD v4, classified as VUS according to ACMG but reported to the family due to consistent phenotype.; Changed rating: GREEN; Changed publications to: 35427807, 36097642, 39945447; Changed phenotypes to: ?Rhizomelic dysplasia, Ain-Naz type, OMIM:619598, rhizomelic dysplasia, Ain-Naz type, MONDO:0859203; Changed mode of inheritance: BIALLELIC, autosomal or pseudoautosomal |
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| Skeletal dysplasia v9.2 | GNPNAT1 | Ida Ertmanska Added comment: Comment on phenotypes: OMIM phenotype updated 11th May 2026. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Skeletal dysplasia v9.2 | GNPNAT1 | Ida Ertmanska Phenotypes for gene: GNPNAT1 were changed from Rhizomelic skeletal dysplasia to ?Rhizomelic dysplasia, Ain-Naz type, OMIM:619598; rhizomelic dysplasia, Ain-Naz type, MONDO:0859203 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Skeletal dysplasia v9.1 | GNPNAT1 | Sadaf Naz reviewed gene: GNPNAT1: Rating: GREEN; Mode of pathogenicity: Other; Publications: 32591345, 35427807, 36097642; Phenotypes: Skeletal dysplasia, Rhizomelic dysplasia, Ain-Naz type; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Skeletal dysplasia v9.1 | GNPNAT1 | Sadaf Naz Deleted their review | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Skeletal dysplasia v9.1 | GNPNAT1 | Sadaf Naz reviewed gene: GNPNAT1: Rating: GREEN; Mode of pathogenicity: Other; Publications: 32591345, 35427807, 36097642; Phenotypes: Skeletal dysplasia, ?Rhizomelic dysplasia, Ain-Naz type; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal; Current diagnostic: yes | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Skeletal dysplasia v2.80 | GNPNAT1 | Michael Oldridge reviewed gene: GNPNAT1: Rating: AMBER; Mode of pathogenicity: None; Publications: 32591345; Phenotypes: rhizomelic short stature; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Skeletal dysplasia v2.11 | GNPNAT1 | Arina Puzriakova Classified gene: GNPNAT1 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Skeletal dysplasia v2.11 | GNPNAT1 | Arina Puzriakova Added comment: Comment on list classification: Amber rating as only one family, but some supporting functional data. Additional cases required to validate pathogenicity of GNPNAT1. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Skeletal dysplasia v2.11 | GNPNAT1 | Arina Puzriakova Gene: gnpnat1 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Skeletal dysplasia v2.10 | GNPNAT1 | Arina Puzriakova edited their review of gene: GNPNAT1: Changed rating: AMBER | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Skeletal dysplasia v2.10 | GNPNAT1 |
Arina Puzriakova changed review comment from: PMID: 32591345 (2020) - Four affected sibs from a consanguineous Pakistani family with skeletal dysplasia, characterised by severe short stature, rhizomelic shortening of the limbs, and metacarpal and metatarsal length irregularities in the hands and feet. WGS revealed a homozygous missense variant (c.226G>A; p.Glu76Lys) in GNPNAT1, which segregating with the phenotype. Gnpnat1 gene knockdown in primary rat chondrocytes decreased cellular proliferation and expression of chondrocyte differentiation markers, indicating the importance of Gnpnat1 for growth plate chondrocyte proliferation and differentiation. Additional cases required to validate pathogenicity of GNPNAT1. Sources: Literature; to: PMID: 32591345 (2020) - Four affected sibs from a consanguineous Pakistani family with skeletal dysplasia, characterised by severe short stature, rhizomelic shortening of the limbs, and metacarpal and metatarsal length irregularities in the hands and feet. WGS revealed a homozygous missense variant (c.226G>A; p.Glu76Lys) in GNPNAT1, which segregating with the phenotype. Gnpnat1 gene knockdown in primary rat chondrocytes decreased cellular proliferation and expression of chondrocyte differentiation markers, indicating the importance of Gnpnat1 for growth plate chondrocyte proliferation and differentiation. Sources: Literature |
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| Skeletal dysplasia v2.10 | GNPNAT1 |
Arina Puzriakova changed review comment from: PMID: 32591345 (2020) - Four affected sibs from a consanguineous Pakistani family with skeletal dysplasia, characterised by severe short stature, rhizomelic shortening of the limbs, and metacarpal and metatarsal length irregularities in the hands and feet. WGS revealed a homozygous missense variant (c.226G>A; p.Glu76Lys) in GNPNAT1, which segregating with the phenotype. Gnpnat1 gene knockdown in primary rat chondrocytes decreased cellular proliferation and expression of chondrocyte differentiation markers, indicating the importance of Gnpnat1 for growth plate chondrocyte proliferation and differentiation. Sources: Literature; to: PMID: 32591345 (2020) - Four affected sibs from a consanguineous Pakistani family with skeletal dysplasia, characterised by severe short stature, rhizomelic shortening of the limbs, and metacarpal and metatarsal length irregularities in the hands and feet. WGS revealed a homozygous missense variant (c.226G>A; p.Glu76Lys) in GNPNAT1, which segregating with the phenotype. Gnpnat1 gene knockdown in primary rat chondrocytes decreased cellular proliferation and expression of chondrocyte differentiation markers, indicating the importance of Gnpnat1 for growth plate chondrocyte proliferation and differentiation. Additional cases required to validate pathogenicity of GNPNAT1. Sources: Literature |
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| Skeletal dysplasia v2.10 | GNPNAT1 |
Arina Puzriakova gene: GNPNAT1 was added gene: GNPNAT1 was added to Skeletal dysplasia. Sources: Literature Mode of inheritance for gene: GNPNAT1 was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: GNPNAT1 were set to 32591345 Phenotypes for gene: GNPNAT1 were set to Rhizomelic skeletal dysplasia Review for gene: GNPNAT1 was set to RED Added comment: PMID: 32591345 (2020) - Four affected sibs from a consanguineous Pakistani family with skeletal dysplasia, characterised by severe short stature, rhizomelic shortening of the limbs, and metacarpal and metatarsal length irregularities in the hands and feet. WGS revealed a homozygous missense variant (c.226G>A; p.Glu76Lys) in GNPNAT1, which segregating with the phenotype. Gnpnat1 gene knockdown in primary rat chondrocytes decreased cellular proliferation and expression of chondrocyte differentiation markers, indicating the importance of Gnpnat1 for growth plate chondrocyte proliferation and differentiation. Sources: Literature |
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