ENDOG p.Pro70=
c.210G>C · rs757963132 · VCV738480
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0504%, nfe)
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 -2.4 | GERP -2.3 |
| Overall | ||
| CADD | 6.846 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0504%
European (non-Finnish) · 563/1,116,066 alleles
Filtering AF
0.0469%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0456%
Overall
0.0412%
603/1,464,706 alleles · ultra-rare
exomes 568/1,312,844 · genomes 35/151,862 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0504% | 1,982 |
| Remaining individualsnot grpmax-eligible | 0.0425% | 2,355 |
| Middle Eastern | 0.0232% | 4,304 |
| Admixed American | 0.0126% | 7,908 |
| African / African-American | 0.00883% | 11,329 |
| South Asian | 0.00524% | 19,089 |
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
- ENDOG
- Protein
- p.Pro70=
- Coding
- c.210G>C
- MANE Select
- NM_004435
- dbSNP
- rs757963132
- Type
- single nucleotide variant
- Location
- chr9:128818894 (GRCh38)
- Gene constraint
- LOEUF 1.847 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 85.67 · 2 PDB
Similar variants
- ENDOG p.Arg184Cys Uncertain significance ★★ ⚠ same type
- ENDOG p.Ile218= Benign ★★ same type
- ENDOG p.Thr246Ile Benign ★★ ⚠ same type
- ENDOG p.Ala130Val Uncertain significance ★ ⚠ same type
- ENDOG p.Ala143Asp Uncertain significance ★ ⚠ same type
- ENDOG p.Ala14Val Uncertain significance ★ ⚠ same type
- ENDOG p.Ala252Val Uncertain significance ★ ⚠ same type
- ENDOG p.Ala284Val 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/endog-p-pro70 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown