Is ERCC4 p.Thr484= (c.1452C>A) pathogenic?

ERCC4 p.Thr484= (c.1452C>A) is classified Likely benign in ERCC4 (ClinVar, Single submitter, 1 submitter; last evaluated 2026-01-11). Very rare (popmax 0.00342%, amr); Associated with Fanconi anemia complementation group Q.

What condition is associated with ERCC4 p.Thr484= (c.1452C>A)?

ERCC4 p.Thr484= (c.1452C>A) is associated with Fanconi anemia complementation group Q, xeroderma pigmentosum group F, Cockayne syndrome (ClinVar).

How common is ERCC4 p.Thr484= (c.1452C>A) in the general population?

ERCC4 p.Thr484= (c.1452C>A) is very rare (popmax 0.00342%, amr) (gnomAD).

ERCC4 p.Thr484=

c.1452C>A · rs1420641422 · VCV1627990

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00342%, amr)

Conditions

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 -1.1	GERP -2.3
Overall
CADD	0.269	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00342% Admixed American · 2/58,490 alleles

Filtering AF 0.000567% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000212%

Overall 0.000373% 6/1,607,180 alleles · very rare

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.00342%	29,245
African / African-American	0.0027%	37,070
Remaining individualsnot grpmax-eligible	0.00161%	62,122
European (non-Finnish)	8.49e-05%	1,178,307

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.Thr484=
Coding: c.1452C>A
MANE Select: NM_005236
dbSNP: rs1420641422
Type: single nucleotide variant
Location: chr16:13935384 (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 484: 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 Cockayne syndrome

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-thr484 (accessed [today's date]).

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