EPHA4 p.Ter987Ser
c.2960G>C · rs1689892062 · VCV3068074
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
Consequence
stop-loss
predicted LoF
gnomAD v4.1
Absent
absent from gnomAD v4.1
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Consequence | stop-loss | predicted loss-of-function in a LoF-intolerant gene |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 7.7 | GERP 2.7, phastCons 1 |
| Overall | ||
| CADD | 17.49 | PHRED · no single calibrated threshold — expert panels disagree |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- EPHA4
- Protein
- p.Ter987Ser
- Coding
- c.2960G>C
- MANE Select
- NM_004438
- dbSNP
- rs1689892062
- Type
- single nucleotide variant
- Location
- chr2:221426029 (GRCh38)
- Gene constraint
- LOEUF 0.256 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 83.93 · 17 PDB
Similar variants
- EPHA4 p.Ala321Thr Uncertain significance ★★ ⚠ same type
- EPHA4 p.Ala852Val Uncertain significance ★★ ⚠ same type
- EPHA4 p.Arg209Cys Uncertain significance ★★ ⚠ same type
- EPHA4 p.Arg230Gln Uncertain significance ★★ ⚠ same type
- EPHA4 p.Arg466Gln Uncertain significance ★★ ⚠ same type
- EPHA4 p.Arg466Trp Uncertain significance ★★ ⚠ same type
- EPHA4 p.Arg486Gln Uncertain significance ★★ ⚠ same type
- EPHA4 p.Arg573Trp 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/epha4-p-ter987ser (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown