NMNAT1

Chr 1

nicotinamide nucleotide adenylyltransferase 1

Also known as: LCA9, NMNAT, PNAT1, SHILCA

NCBI Gene: 64802ENSG00000173614UniProt: Q9HAN9

This gene encodes an enzyme which catalyzes a key step in the biosynthesis of nicotinamide adenine dinucleotide (NAD). The encoded enzyme is one of several nicotinamide nucleotide adenylyltransferases, and is specifically localized to the cell nucleus. Activity of this protein leads to the activation of a nuclear deacetylase that functions in the protection of damaged neurons. Mutations in this gene have been associated with Leber congenital amaurosis 9. Alternative splicing results in multiple transcript variants. Pseudogenes of this gene are located on chromosomes 1, 3, 4, 14, and 15. [provided by RefSeq, Jul 2014]

GeneReviewsResearchGenerating clinical summary…

Primary Disease Associations & Inheritance

UniProtLeber congenital amaurosis 9
UniProtSpondyloepiphyseal dysplasia, sensorineural hearing loss, impaired intellectual development, and Leber congenital amaurosis

Clinical highlights

Gene-disease validity (ClinGen)
NMNAT1-related retinopathy · ARDefinitivesufficient evidence for diagnostic panels
Interpreting a novel variant
Loss of function is the curated mechanism (Gene2Phenotype), though the gene is not strongly LoF-constrained in the population — weigh truncating variants against that tolerance.Curated gene-level mechanism — a prior for triage, not a per-variant call.
0
Active trials
38
Pubs (1 yr)
—
P/LP submissions
—
P/LP missense
0.88
LOEUF
LOF
Mechanism· G2P
📖
GeneReview available — NMNAT1
Authoritative clinical overview · Recommended first read
Open GeneReview ↗
Some data sources returned errors (1)

omim: Error: OMIM fetch failed: 429

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Tolerant — LoF & missense variants common in population
LoF Constraint?
0.88LOEUF
pLI 0.035
Z-score 1.85
OE 0.38 (0.19–0.88)
Tolerant

Typical tolerance to LoF variation

Missense Constraint?
0.63Z-score
OE missense 0.86 (0.74–0.99)
129 obs / 150.6 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios?
LoF OE?0.38 (0.19–0.88)
0≤0.351.4
Missense OE?0.86 (0.74–0.99)
0≤0.61.4
Synonymous OE?0.89
0≤1.21.6
LoF obs/exp: 4 / 10.4Missense obs/exp: 129 / 150.6Syn Z: 0.64

ClinVar Variant Classifications

0 submitted variants in ClinVar

ClinVar

Protein Context — Lollipop Plot

NMNAT1 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →

External Resources

Links to major genomics databases and tools

Franklin by Genoox
AI-powered variant curation and clinical analysis
DECIPHER
Genomic variants and phenotypes in rare disease patients