EFL1 p.Arg441=
c.1323A>G · rs750769187 · VCV1606304
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.0067%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.57 | phastCons 1 |
| Overall | ||
| CADD | 11.0 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0067%
South Asian · 6/89,546 alleles
Filtering AF
0.0029%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00198%
Overall
0.000373%
6/1,606,604 alleles · very rare
exomes 6/1,454,336 · genomes 0/152,268 · joint denominator
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.Arg441=
- Coding
- c.1323A>G
- MANE Select
- NM_024580
- dbSNP
- rs750769187
- Type
- single nucleotide variant
- Location
- chr15:82220199 (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 441
- the 'disordered' region
Similar variants
- 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
- EFL1 p.Arg970Cys 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-arg441 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown