EFL1 p.Pro141=
c.423G>A · rs553252927 · VCV1421371
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00878%, 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 -8.2 | |
| Overall | ||
| CADD | 4.296 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00878%
South Asian · 8/91,068 alleles
Filtering AF
0.00437%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00312%
Overall
0.00105%
17/1,614,024 alleles · very rare
exomes 14/1,461,796 · genomes 3/152,228 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.00878% | 11,384 |
| East Asian | 0.00223% | 44,868 |
| Admixed American | 0.00167% | 60,006 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,502 |
| African / African-American | 0.00133% | 75,018 |
| European (non-Finnish) | 0.000424% | 236,000 |
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.Pro141=
- Coding
- c.423G>A
- MANE Select
- NM_024580
- dbSNP
- rs553252927
- Type
- single nucleotide variant
- Location
- chr15:82240511 (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 141
- the tr-type g domain
Similar variants
- EFL1 p.Pro141Thr Uncertain significance ★★ ⚠ same residue
- EFL1 p.Pro141Leu Uncertain significance ★ ⚠ same residue
- 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
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-pro141 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown