Is ERCC4 p.Thr439fs (c.1315del) pathogenic?

ERCC4 p.Thr439fs (c.1315del) is classified Pathogenic in ERCC4 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-01-01). No gnomAD frequency available for this variant.

How common is ERCC4 p.Thr439fs (c.1315del) in the general population?

ERCC4 p.Thr439fs (c.1315del) is no gnomAD frequency available for this variant (gnomAD).

ERCC4 p.Thr439fs

c.1315del · rs2543180252 · VCV3027158

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function
NMD	predicted	premature termination codon in exon 8 of 11
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 3.4	GERP 0.79, phastCons 1

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: ERCC4
Protein: p.Thr439fs
Coding: c.1315del
MANE Select: NM_005236
dbSNP: rs2543180252
Type: Deletion
Location: chr16:13935244 (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 439: the 'helicase-like' region

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

Similar variants

ERCC4 p.Thr439= Likely benign ★ same residue
ERCC4 p.Arg468fs Pathogenic/Likely pathogenic ★★ same type
ERCC4 p.Asn308fs Pathogenic/Likely pathogenic ★★ same type
ERCC4 p.Glu628fs Pathogenic/Likely pathogenic ★★ same type
ERCC4 p.Phe186fs Pathogenic/Likely pathogenic ★★ same type
ERCC4 p.Thr495fs Pathogenic ★★ same type
ERCC4 c.1905-8_1909del Likely pathogenic ★ same type
ERCC4 p.Ala13fs 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-thr439fs (accessed [today's date]).

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