ERCC4 p.Leu44=
c.132C>T · rs1482378244 · VCV1107762
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.000678%, nfe)
Conditions
3
Fanconi anemia complementation group Q
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 -0.38 | GERP -1.3, phastCons 0.082 |
| Overall | ||
| CADD | 9.66 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000678%
European (non-Finnish) · 8/1,179,746 alleles
Filtering AF
0.000292%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000211%
Overall
0.000551%
8/1,451,796 alleles · very rare
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
- ERCC4
- Protein
- p.Leu44=
- Coding
- c.132C>T
- MANE Select
- NM_005236
- dbSNP
- rs1482378244
- Type
- single nucleotide variant
- Location
- chr16:13920297 (GRCh38)
- Gene constraint
- LOEUF 0.984 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 74.60 · 13 PDB
- Residue 44
- the 'helicase-like' region
Similar variants
- ERCC4 p.Leu44Phe Uncertain significance ★ ⚠ same residue
- ERCC4 c.1102+1G>T Likely pathogenic ★★ same condition
- ERCC4 c.793-2A>G Pathogenic ★★ same condition
- ERCC4 p.Arg20Ter Pathogenic ★★ same condition
- ERCC4 p.Arg589Trp Pathogenic/Likely pathogenic ★★ same condition
- ERCC4 p.Arg689Ser Likely pathogenic ★★ same condition
- ERCC4 p.Arg772Ter Pathogenic/Likely pathogenic ★★ same condition
- ERCC4 p.Cys236Arg Pathogenic/Likely pathogenic ★★ same condition
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/ercc4-p-leu44 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown