NADSYN1

Chr 11AR

NAD synthetase 1

Also known as: VCRL3

NAD synthetase catalyzes the final step in nicotinamide adenine dinucleotide (NAD) biosynthesis, converting deamido-NAD to NAD using ATP and glutamine. Mutations cause vertebral, cardiac, renal, and limb defects syndrome 3, a congenital malformation disorder with autosomal recessive inheritance. The gene shows tolerance to loss-of-function variants (low constraint), consistent with the recessive inheritance pattern observed clinically.

GeneReviewsOMIMResearchSummary from RefSeq, OMIM, UniProt
LOFmechanismARLOEUF 0.941 OMIM phenotype
Clinical SummaryNADSYN1
Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
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GeneReview available — NADSYN1
Authoritative clinical overview · Recommended first read
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Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

Tolerant — LoF & missense variants common in population
LoF Constraint
0.94LOEUF
pLI 0.000
Z-score 1.89
OE 0.70 (0.530.94)
Tolerant

Typical tolerance to LoF variation

Missense Constraint
0.71Z-score
OE missense 0.91 (0.830.98)
407 obs / 449.4 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios
LoF OE0.70 (0.530.94)
00.351.4
Missense OE0.91 (0.830.98)
00.61.4
Synonymous OE1.09
01.21.6
LoF obs/exp: 32 / 45.8Missense obs/exp: 407 / 449.4Syn Z: -1.01
Curated Mechanism (G2P)Gene2Phenotype (DDG2P) ↗
strongNADSYN1-related congenital NAD deficiency disorderLOFAR

Predictions shown for reference only — model trained on dominant genes, not applicable to AR conditions.

DN
0.7230th %ile
GOF
0.5268th %ile
LOF
0.3162th %ile

The Badonyi & Marsh prediction model was trained exclusively on dominant disease genes. Predictions are not reliable for genes with autosomal recessive inheritance and are shown at reduced opacity for reference only.

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312.

ClinVar Variant Classifications

0 submitted variants in ClinVar

Protein Context — Lollipop Plot

NADSYN1 · protein map & ClinVar variants

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

3D Protein StructureAlphaFold

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

No active trials found for this gene.

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Clinical Literature
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Full-Text Mentions
NLP-detected gene mentions in article bodies · via PubTator3
PubTator3
Top 3 full-text resultsSearch PubTator3 ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC