NT5E p.Asp513=
c.1539T>C · rs150989796 · VCV735452
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0613%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.016 | strongly benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -5.5 | GERP -4.5 |
| Overall | ||
| CADD | 0.801 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0613%
African / African-American · 46/75,044 alleles
Filtering AF
0.0471%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0422%
Overall
0.00335%
54/1,614,112 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0613% | 1,631 |
| Middle Eastern | 0.0165% | 6,062 |
| Remaining individualsnot grpmax-eligible | 0.0048% | 20,836 |
| Admixed American | 0.00333% | 30,010 |
| European (non-Finnish) | 0.000169% | 589,984 |
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
- NT5E
- Protein
- p.Asp513=
- Coding
- c.1539T>C
- MANE Select
- NM_002526
- dbSNP
- rs150989796
- Type
- single nucleotide variant
- Location
- chr6:85492155 (GRCh38)
- Gene constraint
- LOEUF 1.254 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 91.95 · 52 PDB
- Residue 513
- an α-helix
Similar variants
- NT5E c.1210+12G>C Benign ★★ same type
- NT5E p.Gly148= Likely benign ★★ same type
- NT5E p.Thr376Ala Benign ★★ same type
- NT5E p.Thr407= Benign/Likely benign ★★ same type
- NT5E c.1104+2T>A Likely pathogenic ★ same type
- NT5E p.Cys476Ter Likely pathogenic ★ same type
- NT5E c.562+1G>T Uncertain significance ★ same type
- NT5E p.Ala10Pro 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/nt5e-p-asp513 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown