EFL1 p.Ala175=
c.525G>A · rs955621188 · VCV3057624
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00267%, afr)
Conditions
1
EFL1-related disorder
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.25 | acceptor loss · deltas |
|---|---|---|
| Pangolin | Δ0.24 | gain · loss 0.16 · SpliceAI calls loss · independent |
| Constraint at this position | ||
| Conservation | phyloP -0.1 | phastCons 0.82 |
| Overall | ||
| CADD | 12.55 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00267%
African / African-American · 2/74,852 alleles
Filtering AF
0.00069%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00054%
Overall
0.00112%
18/1,609,426 alleles · very rare
exomes 18/1,457,240 · genomes 0/152,186 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00267% | 37,426 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,320 |
| European (non-Finnish) | 0.00119% | 84,108 |
| South Asian | 0.00111% | 90,346 |
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
- EFL1
- Protein
- p.Ala175=
- Coding
- c.525G>A
- MANE Select
- NM_024580
- dbSNP
- rs955621188
- Type
- single nucleotide variant
- Location
- chr15:82238513 (GRCh38)
- Gene constraint
- LOEUF 0.718 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 74.72 · 2 PDB
- Residue 175
- the tr-type g domain
Disease context
EFL1-related disorder
Similar variants
- EFL1 p.Asp284= Likely benign same condition
- EFL1 c.1444+3A>C Uncertain significance ★★ same type
- EFL1 c.244+2T>G Uncertain significance ★★ same type
- EFL1 p.Ala755Thr Uncertain significance ★★ ⚠ same type
- EFL1 p.Arg108His Uncertain significance ★★ ⚠ same type
- EFL1 p.Arg1097Trp Uncertain significance ★★ ⚠ same type
- EFL1 p.Arg330Trp Uncertain significance ★★ ⚠ same type
- EFL1 p.Arg444His 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/efl1-p-ala175 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown