ENTPD1 p.His474=
c.1422C>T · rs746932318 · VCV2640720
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00659%, sas)
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 -1.8 | GERP -5.2 |
| Overall | ||
| CADD | 0.504 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00659%
South Asian · 6/91,084 alleles
Filtering AF
0.00286%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00195%
Overall
0.000479%
7/1,461,884 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.00659% | 15,181 |
| European (non-Finnish) | 8.47e-05% | 1,180,045 |
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
- ENTPD1
- Protein
- p.His474=
- Coding
- c.1422C>T
- MANE Select
- NM_001776
- dbSNP
- rs746932318
- Type
- single nucleotide variant
- Location
- chr10:95866272 (GRCh38)
- Gene constraint
- LOEUF 0.737 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 90.85
Similar variants
- ENTPD1 p.Leu370Ter Pathogenic ★★ same type
- ENTPD1 p.Tyr287Ter Pathogenic ★★ same type
- ENTPD1 p.Ala236Ser Uncertain significance ★★ ⚠ same type
- ENTPD1 p.Arg147Ser Uncertain significance ★★ ⚠ same type
- ENTPD1 p.Glu140Ala Uncertain significance ★★ ⚠ same type
- ENTPD1 p.Glu142Gln Uncertain significance ★★ ⚠ same type
- ENTPD1 p.Glu231Lys Uncertain significance ★★ ⚠ same type
- ENTPD1 p.Glu380Gly 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/entpd1-p-his474 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown