NT5C2 p.Val169del
c.503TAG[1] · rs762980266 · VCV432907
Likely pathogenic
Single submitter
Classification
Likely pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00026%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 7.9 | GERP 2.5, phastCons 1 |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00026%
European (non-Finnish) · 3/1,153,866 alleles
Filtering AF
6.9e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.9e-05%
Overall
0.000209%
3/1,433,028 alleles · very rare
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
- NT5C2
- Protein
- p.Val169del
- Coding
- c.503TAG[1]
- MANE Select
- NM_001351169
- dbSNP
- rs762980266
- Type
- Microsatellite
- Location
- chr10:103101076 (GRCh38)
- Gene constraint
- LOEUF 1.128 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 88.81 · 43 PDB
- Residue 169
- an α-helix
Similar variants
- NT5C2 p.Leu105fs Pathogenic/Likely pathogenic ★★ same type
- NT5C2 c.175+3086_175+3087del Uncertain significance ★ same type
- NT5C2 c.539+5_539+8del 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/nt5c2-p-val169del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown