Is ERCC4 p.Ser521Arg (c.1563C>G) pathogenic?

ERCC4 p.Ser521Arg (c.1563C>G) is classified Conflicting classifications of pathogenicity in ERCC4 (ClinVar, Conflicting submitters, 16 submitters; last evaluated 2026-02-01). AlphaMissense: likely benign (0.2971); Rare (popmax 0.298%, amr); Associated with Fanconi anemia complementation group Q.

What condition is associated with ERCC4 p.Ser521Arg (c.1563C>G)?

ERCC4 p.Ser521Arg (c.1563C>G) is associated with Fanconi anemia complementation group Q, xeroderma pigmentosum group F, XFE progeroid syndrome (ClinVar).

How common is ERCC4 p.Ser521Arg (c.1563C>G) in the general population?

ERCC4 p.Ser521Arg (c.1563C>G) is rare (popmax 0.298%, amr) (gnomAD).

What do computational predictors say about ERCC4 p.Ser521Arg (c.1563C>G)?

AlphaMissense predicts likely benign (score 0.2971) — an in-silico prediction, not a clinical call.

ERCC4 p.Ser521Arg

c.1563C>G · rs41552412 · VCV134153

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 16 submitters

AlphaMissense

likely benign

0.2971 · ACMG-weighted

gnomAD v4.1

Rare

rare (popmax 0.298%, amr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Fanconi anemia complementation group Q

Computational evidence

Protein change
AlphaMissense	0.2971	likely benign
REVEL	0.11	moderately benign-leaning
SaProt	LLR -9.32	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 2.6	GERP 1.5, phastCons 1
Regional constraint	o/e 1.08	unconstrained · MANE · 28 kb · p 0.011 · regional, not allelic
Overall
CADD	18.42	PHRED · no single calibrated threshold — expert panels disagree

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

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.298% Admixed American · 179/60,014 alleles

Filtering AF 0.262% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.249%

Overall 0.124% 2,006/1,614,058 alleles · rare

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.298%	335
Remaining individualsnot grpmax-eligible	0.157%	638
European (non-Finnish)	0.145%	688
African / African-American	0.0173%	5,770
Middle Eastern	0.0165%	6,062
Finnishnot grpmax-eligible	0.00156%	64,010

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.Ser521Arg
Coding: c.1563C>G
MANE Select: NM_005236
dbSNP: rs41552412
Type: single nucleotide variant
Location: chr16:13935495 (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 521: a modified residue (phosphoserine); the 'disordered' region

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

Disease context

Fanconi anemia complementation group Q — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: xeroderma pigmentosum group F XFE progeroid syndrome hereditary neoplastic syndrome Cockayne syndrome xeroderma pigmentosum

Similar variants

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
ERCC4 p.Cys723Ter 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-ser521arg (accessed [today's date]).

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