ENTREP1 p.Ala396=
c.1188C>T · rs531379531 · VCV514991
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0187%, eas)
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 1.9 | GERP -2.8, phastCons 1 |
| Overall | ||
| CADD | 9.698 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0187%
East Asian · 8/42,792 alleles
Filtering AF
0.00921%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00678%
Overall
0.00216%
34/1,571,760 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0187% | 5,349 |
| Middle Eastern | 0.0185% | 5,408 |
| Admixed American | 0.0111% | 9,039 |
| Remaining individualsnot grpmax-eligible | 0.00492% | 20,313 |
| European (non-Finnish) | 0.00138% | 72,716 |
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
- ENTREP1
- Protein
- p.Ala396=
- Coding
- c.1188C>T
- MANE Select
- NM_001347995
- dbSNP
- rs531379531
- Type
- single nucleotide variant
- Location
- chr9:69385820 (GRCh38)
- Structure
- AlphaFold pLDDT 60.47
- Residue 396
- the 'mediates interaction with epn1' region
Similar variants
- ENTREP1 p.Ala374Ser Uncertain significance ★ ⚠ same type
- ENTREP1 p.Ala418Asp Uncertain significance ★ ⚠ same type
- ENTREP1 p.Ala440Ser Uncertain significance ★ ⚠ same type
- ENTREP1 p.Ala440Thr Uncertain significance ★ ⚠ same type
- ENTREP1 p.Ala448Ser Uncertain significance ★ ⚠ same type
- ENTREP1 p.Ala492Val Uncertain significance ★ ⚠ same type
- ENTREP1 p.Ala574Pro Uncertain significance ★ ⚠ same type
- ENTREP1 p.Ala588Val Conflicting classifications of pathogenicity ★ ⚠ 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/entrep1-p-ala396 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown