ELF4 p.Ala95=
c.285G>A · VCV4688972
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0474%, eas)
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 -0.97 | GERP -3.5 |
| Overall | ||
| CADD | 0.357 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0474%
East Asian · 16/33,762 alleles
Filtering AF
0.0297%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0241%
Overall
0.00661%
80/1,209,783 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0474% | 2,110 |
| African / African-American | 0.0228% | 4,390 |
| Remaining individualsnot grpmax-eligible | 0.0126% | 7,934 |
| Admixed American | 0.00875% | 11,434 |
| South Asian | 0.00704% | 14,204 |
| European (non-Finnish) | 0.00413% | 24,194 |
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
- ELF4
- Protein
- p.Ala95=
- Coding
- c.285G>A
- MANE Select
- NM_001421
- Type
- single nucleotide variant
- Location
- chrX:130074104 (GRCh38)
- Structure
- AlphaFold pLDDT 49.77
- Residue 95
- a UniProt-annotated variant site (no effect on transcriptional activity shown in ifnb1 promoter-driven luciferase assay); the 'runx1-binding' region
Similar variants
- ELF4 p.Ala95Thr Likely benign ★ same residue
- ELF4 p.Gly206Asp Uncertain significance ★★ ⚠ same type
- ELF4 p.Ser413Leu Uncertain significance ★★ ⚠ same type
- ELF4 p.Ala147Val Benign/Likely benign ★★ same type
- ELF4 p.Arg604Cys Benign ★★ same type
- ELF4 p.Ser369= Benign ★★ same type
- ELF4 p.Thr503= Benign ★★ same type
- ELF4 p.Arg185Ter Likely pathogenic ★ 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/elf4-p-ala95 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown