EPHA10 p.Pro534=
c.1602G>A · rs77925917 · VCV2638680
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
rare (popmax 0.144%, 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 -12 | GERP -4 |
| Overall | ||
| CADD | 0.923 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.144%
African / African-American · 108/75,006 alleles
Filtering AF
0.122%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.114%
Overall
0.0114%
184/1,613,928 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.144% | 695 |
| Middle Eastern | 0.0165% | 6,060 |
| Remaining individualsnot grpmax-eligible | 0.0144% | 6,945 |
| Admixed American | 0.01% | 9,999 |
| South Asian | 0.00659% | 15,175 |
| East Asian | 0.00446% | 22,430 |
| European (non-Finnish) | 0.00432% | 23,136 |
| Finnishnot grpmax-eligible | 0.00156% | 64,030 |
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
- EPHA10
- Protein
- p.Pro534=
- Coding
- c.1602G>A
- MANE Select
- NM_001099439
- dbSNP
- rs77925917
- Type
- single nucleotide variant
- Location
- chr1:37731472 (GRCh38)
- Gene constraint
- LOEUF 1.481 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 79.56
- Residue 534
- the fibronectin type-iii 2 domain
Similar variants
- EPHA10 p.Ala532Thr Benign ★★ same type
- EPHA10 p.Ser574Leu Benign ★★ same type
- EPHA10 p.Ala200Ser Uncertain significance ★ ⚠ same type
- EPHA10 p.Ala200Val Uncertain significance ★ ⚠ same type
- EPHA10 p.Ala213Thr Uncertain significance ★ ⚠ same type
- EPHA10 p.Ala323Glu Uncertain significance ★ ⚠ same type
- EPHA10 p.Ala388Thr Uncertain significance ★ ⚠ same type
- EPHA10 p.Ala403Glu 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/epha10-p-pro534 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown