ENTREP1 p.Cys565=
c.1695C>T · rs36097736 · VCV678698
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 3.81%, afr)
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 -8 | GERP -3.4 |
| Overall | ||
| CADD | 0.149 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
3.81%
African / African-American · 2,857/75,046 alleles
Filtering AF
3.69%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 3.64%
Overall
0.209%
3,376/1,614,114 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 3.81% | 26 |
| Remaining individualsnot grpmax-eligible | 0.314% | 319 |
| Admixed American | 0.265% | 378 |
| Middle Eastern | 0.165% | 606 |
| South Asian | 0.022% | 4,554 |
| European (non-Finnish) | 0.011% | 9,077 |
| East Asian | 0.00446% | 22,434 |
| Finnishnot grpmax-eligible | 0.00312% | 32,004 |
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.Cys565=
- Coding
- c.1695C>T
- MANE Select
- NM_001347995
- dbSNP
- rs36097736
- Type
- single nucleotide variant
- Location
- chr9:69391687 (GRCh38)
- Structure
- AlphaFold pLDDT 60.47
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-cys565 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown