NAPRT p.Asp320=
c.960C>T · rs36121778 · VCV780131
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 3.55%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 5.8 | GERP 1.1, phastCons 1 |
| Overall | ||
| CADD | 7.968 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
3.55%
African / African-American · 2,659/74,988 alleles
Filtering AF
3.43%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 3.39%
Overall
0.263%
4,236/1,612,574 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 3.55% | 28 |
| Middle Eastern | 0.859% | 116 |
| Admixed American | 0.559% | 179 |
| Remaining individualsnot grpmax-eligible | 0.456% | 219 |
| Ashkenazi Jewishnot grpmax-eligible | 0.45% | 222 |
| European (non-Finnish) | 0.0643% | 1,554 |
| South Asian | 0.0132% | 7,588 |
| East Asian | 0.00223% | 44,862 |
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- NAPRT
- Protein
- p.Asp320=
- Coding
- c.960C>T
- MANE Select
- NM_145201
- dbSNP
- rs36121778
- Type
- single nucleotide variant
- Location
- chr8:143576494 (GRCh38)
- Gene constraint
- LOEUF 1.486 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 94.94 · 1 PDB
Similar variants
- NAPRT c.1447-7C>G Benign ★★ same type
- NAPRT p.Pro117= Benign/Likely benign ★★ same type
- NAPRT p.Ala13Gly Uncertain significance ★ ⚠ same type
- NAPRT p.Ala159Thr Uncertain significance ★ ⚠ same type
- NAPRT p.Ala231Val Uncertain significance ★ ⚠ same type
- NAPRT p.Ala234Pro Uncertain significance ★ ⚠ same type
- NAPRT p.Ala23Thr Uncertain significance ★ ⚠ same type
- NAPRT p.Ala243Val Uncertain significance ★ ⚠ same type
Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →
Cite Sugi Variant
Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/naprt-p-asp320 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown