ENTPD6 p.Phe428=
c.1284C>T · rs73339100 · VCV790770
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 2.44%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.416 | indeterminate |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -1.5 | GERP -4.3 |
| Overall | ||
| CADD | 1.066 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
2.44%
African / African-American · 1,831/75,024 alleles
Filtering AF
2.35%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 2.31%
Overall
0.129%
2,084/1,613,598 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 2.44% | 41 |
| Remaining individualsnot grpmax-eligible | 0.171% | 584 |
| Middle Eastern | 0.165% | 606 |
| Admixed American | 0.12% | 833 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0338% | 2,959 |
| European (non-Finnish) | 0.00449% | 22,263 |
| South Asian | 0.0011% | 91,020 |
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
- ENTPD6
- Protein
- p.Phe428=
- Coding
- c.1284C>T
- MANE Select
- NM_001247
- dbSNP
- rs73339100
- Type
- single nucleotide variant
- Location
- chr20:25225245 (GRCh38)
- Gene constraint
- LOEUF 0.949 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 83.21
- Residue 428
- a disulfide bond
Similar variants
- ENTPD6 p.Val436Ile Likely benign ★★ same type
- ENTPD6 p.Ala305Val Uncertain significance ★ ⚠ same type
- ENTPD6 p.Ala337Thr Uncertain significance ★ ⚠ same type
- ENTPD6 p.Ala390Val Uncertain significance ★ ⚠ same type
- ENTPD6 p.Ala397Val Uncertain significance ★ ⚠ same type
- ENTPD6 p.Ala411Thr Uncertain significance ★ ⚠ same type
- ENTPD6 p.Ala67Thr Uncertain significance ★ ⚠ same type
- ENTPD6 p.Ala77Gly 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/entpd6-p-phe428 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown