Is ERCC4 p.Lys915Glu (c.2743A>G) pathogenic?

ERCC4 p.Lys915Glu (c.2743A>G) is classified Uncertain significance in ERCC4 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-11-20). AlphaMissense: likely benign (0.0932); Very rare (popmax 0.00212%, nfe).

How common is ERCC4 p.Lys915Glu (c.2743A>G) in the general population?

ERCC4 p.Lys915Glu (c.2743A>G) is very rare (popmax 0.00212%, nfe) (gnomAD).

What do computational predictors say about ERCC4 p.Lys915Glu (c.2743A>G)?

AlphaMissense predicts likely benign (score 0.0932) — an in-silico prediction, not a clinical call.

ERCC4 p.Lys915Glu

c.2743A>G · VCV3364396

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0932 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00212%, nfe)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0932	likely benign
REVEL	0.16	moderately benign-leaning
SaProt	LLR -9.53	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 5.8	GERP 2, phastCons 1
Regional constraint	o/e 1.08	unconstrained · MANE · 28 kb · p 0.011 · regional, not allelic
Overall
CADD	17.81	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00212% European (non-Finnish) · 25/1,179,950 alleles

Filtering AF 0.00145% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00123%

Overall 0.00185% 27/1,458,112 alleles · very rare

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.00212%	47,198
Remaining individualsnot grpmax-eligible	0.0016%	62,488
African / African-American	0.00133%	75,054

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.Lys915Glu
Coding: c.2743A>G
MANE Select: NM_005236
Type: single nucleotide variant
Location: chr16:13948339 (GRCh38)
Gene constraint: LOEUF 0.984 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 74.60 · 13 PDB

Full ERCC4 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

ERCC4 p.Lys915Arg Conflicting classifications of pathogenicity ★ ⚠ same residue
ERCC4 c.1102+1G>T Likely pathogenic ★★ same type
ERCC4 c.793-2A>G Pathogenic ★★ same type
ERCC4 p.Arg20Ter Pathogenic ★★ same type
ERCC4 p.Arg589Trp Pathogenic/Likely pathogenic ★★ same type
ERCC4 p.Arg689Ser Likely pathogenic ★★ same type
ERCC4 p.Arg772Ter Pathogenic/Likely pathogenic ★★ same type
ERCC4 p.Cys236Arg Pathogenic/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/ercc4-p-lys915glu (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown