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Fetal anomalies

Gene: NMNAT1

Amber List (moderate evidence)
NMNAT1 (nicotinamide nucleotide adenylyltransferase 1)
EnsemblGeneIds (GRCh38): ENSG00000173614
EnsemblGeneIds (GRCh37): ENSG00000173614
OMIM: 608700, Gene2Phenotype
NMNAT1 is in 5 panels

3 reviews

Arina Puzriakova (Genomics England Curator)

I don't know

Upgraded from Red to Amber, 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: 6.29

Natalie Chandler (North Thames GLH)

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
Reviewed in 2019 and decided phenotype not fetally relevant. Also not on Aus panel. Amber on Skeletal panel as 2 of 3cases are related but on the watchlist PMID:32533184 reported two distantly related families homozygous for 7.4-kb duplication involving the last 2 exons of the NMNAT1 gene (chr1:10,036,359-10,043,727, GRCh37).PMID:33668384 reported a 2-year-old girl compound heterozygous for the duplication and with a splicing variant (c.439+5G>T).These patients presented with a severe form of spondylo-epiphyseal dysplasia, sensorineural hearing loss, intellectual disability, Leber congenital amaurosis and several brain abnormalities. Presented at 5 days with short stature and absence of bone spicules, brain MRI evere hypomyelination and signs of brain atrophy, measured as brain volume loss, with mild ventricular expansion, subarachnoid space increase and severe corpus callosum hypoplasia. PMID 39891418 hom missense variant. Fetus had Short limbs, severe corpus callosum hypoplasia, cerebellar hypoplasia, dysmorphic facies with depressed nasal bridge. Fetal paper but no gestation. Amber/Green
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
Spondyloepiphyseal dysplasia, sensorineural hearing loss, intellectual developmental disorder, and Leber congenital amaurosis

Publications

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

Rebecca Foulger (Genomics England curator)

Red List (low evidence)

This gene and phenotype were reviewed during meetings at Great Ormond Street hospital in March 2019. Clinical review and curation was performed by Lyn Chitty, Anna de Burca, Rhiannon Mellis, Richard Scott, Ellen McDonagh and Rebecca Foulger. Outcome of review: Phenotype is not fetally-relevant. Action taken: Demoted NMNAT1 gene rating from Green to Red.
Created: 24 Mar 2019, 4:30 p.m.
DDG2P rating in original PAGE list: Confirmed for LEBER CONGENITAL AMAUROSIS
Created: 11 Dec 2018, 9:05 a.m.
Created: 11 Dec 2018, 9:05 a.m.

Panel version: 0.134

Details

Mode of Inheritance
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert Review Amber
  • PAGE DD-Gene2Phenotype
Phenotypes
  • Spondyloepiphyseal dysplasia, sensorineural hearing loss, intellectual developmental disorder, and Leber congenital amaurosis
  • LEBER CONGENITAL AMAUROSIS
OMIM
608700
Clinvar variants
Variants in NMNAT1
Penetrance
None
Publications
Panels with this gene

History Filter Activity

5 Sep 2025, Gel status: 2

Added New Source, Set Phenotypes, Set publications, Status Update

Arina Puzriakova (Genomics England Curator)

Source Expert Review Amber was added to NMNAT1. Added phenotypes Spondyloepiphyseal dysplasia, sensorineural hearing loss, intellectual developmental disorder, and Leber congenital amaurosis for gene: NMNAT1 Publications for gene: NMNAT1 were updated from to 39891418 Rating Changed from Red List (low evidence) to Amber List (moderate evidence)

24 Mar 2019, Gel status: 1

Added New Source, Status Update

Rebecca Foulger (Genomics England curator)

Source Expert Review Red was added to NMNAT1. Rating Changed from Green List (high evidence) to Red List (low evidence)

8 Nov 2018, Gel status: 4

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

Rebecca Foulger (Genomics England curator)

gene: NMNAT1 was added gene: NMNAT1 was added to Fetal anomalies. Sources: Expert Review Green,PAGE DD-Gene2Phenotype Mode of inheritance for gene: NMNAT1 was set to BIALLELIC, autosomal or pseudoautosomal Phenotypes for gene: NMNAT1 were set to LEBER CONGENITAL AMAUROSIS