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Fetal anomalies

Gene: GNPNAT1

Amber List (moderate evidence)
GNPNAT1 (glucosamine-phosphate N-acetyltransferase 1)
EnsemblGeneIds (GRCh38): ENSG00000100522
EnsemblGeneIds (GRCh37): ENSG00000100522
OMIM: 616510, Gene2Phenotype
GNPNAT1 is in 2 panels

4 reviews

Ida Ertmanska (Genomics England Curator)

Green List (high evidence)

Comment on list classification: There are now 4 unrelated individuals reported with biallelic GNPNAT1 missense variants and skeletal dysplasia, which is detectable on fetal ultrasound. Hence, this gene should be promoted to Green at the next update.
Created: 11 May 2026, 4:29 p.m. | Last Modified: 11 May 2026, 4:29 p.m.
Panel Version: 7.3
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.
Created: 11 May 2026, 4:23 p.m. | Last Modified: 11 May 2026, 4:23 p.m.
Panel Version: 7.3

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

Phenotypes
?Rhizomelic dysplasia, Ain-Naz type, OMIM:619598; rhizomelic dysplasia, Ain-Naz type, MONDO:0859203

Publications

Created: 11 May 2026, 4:23 p.m.
Last Modified: 11 May 2026, 4:23 p.m.
Panel version: 7.3

Beth Young (West Midlands Regional Genetics Laboratory)

I don't know

Amber on skeletal dysplasia and FA panels. Amber on Australian FA Panel. No new literature to support upgrade since last review in Sept 2025.
Created: 10 Mar 2026, 11:27 a.m. | Last Modified: 10 Mar 2026, 11:27 a.m.
Panel Version: 6.147

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

Phenotypes
Talipes equinovarus

Publications

Created: 10 Mar 2026, 11:27 a.m.
Last Modified: 10 Mar 2026, 11:27 a.m.
Panel version: 6.147

Arina Puzriakova (Genomics England Curator)

I don't know

This gene and phenotype were reviewed during meetings between November 2025 & January 2026. The meetings included representatives of the Central & South and North Thames R21 testing GLHs and from the R21 Clinical Oversight Group. Clinical review and curation was performed by Stephanie Allen, Elizabeth Young and Sarah Graham (Central & South GLH), Natalie Chandler and Elizabeth Scotchman (North Thames GLH), and Tazeen Ashraf, Anna De Burca, Natalie Canham, Samantha Doyle, Alice Gardham, Victoria Harrison, Tessa Homfray, Esther Kinning, and Soo-Mi Park (R21 Clinical Oversight Group).
Created: 10 Mar 2026, 11:35 a.m. | Last Modified: 10 Mar 2026, 11:35 a.m.
Panel Version: 6.148
New gene added to this panel with an Amber rating, inline with the recent review by the R21 Clinical Oversight Group.
Created: 5 Sep 2025, 4:41 p.m. | Last Modified: 5 Sep 2025, 4:41 p.m.
Panel Version: 6.29
Created: 5 Sep 2025, 4:41 p.m.
Last Modified: 5 Sep 2025, 4:41 p.m.
Panel version: 6.148

Vicki Harrison (Wessex Clinical Genetics Service)

I don't know

This gene and phenotype were reviewed during meetings in June & July 2025. The meetings included representatives of the North Thames and Central & South R21 testing GLHs and from the R21 Clinical Oversight Group. Clinical review and curation was performed by Natalie Chandler & Elizabeth Scotchman (North Thames GLH), Natalie Bibb, Stephanie Allen & Sarah Graham (Central & South GLH) and Alice Gardham, Esther Kinning, Vicki Harrison, Anna DeBurca, Natalie Canham, Elizabeth Wall, Sunayna Best, Soo-Mi Park & Sahar Mansour (R21 Clinical Oversight Group).
Created: 5 Sep 2025, 4:31 p.m. | Last Modified: 5 Sep 2025, 4:31 p.m.
Panel Version: 6.28
Pan et al. One fetus with talipes, nuchal thickening, short limbs, narrow thorax, biallelic variant, VUS initially. Previous affected pregnancy confirmed to have same variants. Ul Ain et al. 4 sibs from same Pakistani family all assessed in their 40s, no comment about age of onset, severe disproportionate short stature, rhizomelic. Platyspondyly, hip dysplasia, abnormal metaphyses. Normal cognition. Mouse knockouts. Similar role as PGM3 already green in R21 panel. This gene felt to be be similar but more severe. No anaemia or immune dysfuntion though. Amber
Created: 5 Sep 2025, 2:55 p.m. | Last Modified: 5 Sep 2025, 2:55 p.m.
Panel Version: 6.24

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

Phenotypes
Rhizomelic dysplasia, Ain-Naz type

Publications

Created: 5 Sep 2025, 2:55 p.m.
Last Modified: 5 Sep 2025, 2:55 p.m.
Panel version: 6.28

Details

Mode of Inheritance
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert Review Amber
Phenotypes
  • Talipes equinovarus
  • ?Rhizomelic dysplasia, Ain-Naz type, OMIM:619598
  • rhizomelic dysplasia, Ain-Naz type, MONDO:0859203
Tags
Q2_26_promote_green
OMIM
616510
Clinvar variants
Variants in GNPNAT1
Penetrance
None
Publications
Panels with this gene

History Filter Activity

11 May 2026, Gel status: 2

Set Phenotypes

Ida Ertmanska (Genomics England Curator)

Phenotypes for gene: GNPNAT1 were changed from Talipes equinovarus; Rhizomelic dysplasia, Ain-Naz type to Talipes equinovarus; ?Rhizomelic dysplasia, Ain-Naz type, OMIM:619598; rhizomelic dysplasia, Ain-Naz type, MONDO:0859203

11 May 2026, Gel status: 2

Set publications

Ida Ertmanska (Genomics England Curator)

Publications for gene: GNPNAT1 were set to 39945447

11 May 2026, Gel status: 2

Added Tag

Ida Ertmanska (Genomics England Curator)

Tag Q2_26_promote_green tag was added to gene: GNPNAT1.

10 Mar 2026, Gel status: 2

Set Phenotypes

Arina Puzriakova (Genomics England Curator)

Added phenotypes Talipes equinovarus for gene: GNPNAT1

5 Sep 2025, Gel status: 2

Created, Added New Source, Set mode of inheritance, Set publications, Set Phenotypes

Arina Puzriakova (Genomics England Curator)

gene: GNPNAT1 was added gene: GNPNAT1 was added to Fetal anomalies. Sources: Expert Review Amber Mode of inheritance for gene: GNPNAT1 was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: GNPNAT1 were set to 39945447 Phenotypes for gene: GNPNAT1 were set to Rhizomelic dysplasia, Ain-Naz type