EPHA7 p.Ser427=
c.1281C>T · rs56140608 · VCV2656777
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.536%, sas)
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 2.5 | GERP -2.2, phastCons 1 |
| Overall | ||
| CADD | 8.095 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.536%
South Asian · 488/91,040 alleles
Filtering AF
0.497%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.481%
Overall
0.26%
4,191/1,613,848 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.536% | 187 |
| Middle Eastern | 0.314% | 319 |
| Finnishnot grpmax-eligible | 0.286% | 350 |
| Remaining individualsnot grpmax-eligible | 0.278% | 359 |
| European (non-Finnish) | 0.275% | 364 |
| Amishnot grpmax-eligible | 0.219% | 456 |
| Admixed American | 0.07% | 1,429 |
| African / African-American | 0.0493% | 2,028 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00676% | 14,785 |
| East Asian | 0.00223% | 44,864 |
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
- EPHA7
- Protein
- p.Ser427=
- Coding
- c.1281C>T
- MANE Select
- NM_004440
- dbSNP
- rs56140608
- Type
- single nucleotide variant
- Location
- chr6:93356760 (GRCh38)
- Gene constraint
- LOEUF 0.282 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 82.09 · 7 PDB
- Residue 427
- the fibronectin type-iii 1 domain
Similar variants
- EPHA7 c.2111-2A>G Uncertain significance ★ same type
- EPHA7 p.Ala191Ser Uncertain significance ★ ⚠ same type
- EPHA7 p.Ala27Glu Uncertain significance ★ ⚠ same type
- EPHA7 p.Ala520Asp Uncertain significance ★ ⚠ same type
- EPHA7 p.Ala721Ser Uncertain significance ★ ⚠ same type
- EPHA7 p.Ala721Val Uncertain significance ★ ⚠ same type
- EPHA7 p.Ala761Val Uncertain significance ★ ⚠ same type
- EPHA7 p.Ala986Val 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/epha7-p-ser427 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown