Is ERCC4 c.2017+19del pathogenic?

ERCC4 c.2017+19del is classified Likely benign in ERCC4 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-07-25). Absent from gnomAD; Associated with xeroderma pigmentosum group F.

What condition is associated with ERCC4 c.2017+19del?

ERCC4 c.2017+19del is associated with xeroderma pigmentosum group F, Fanconi anemia complementation group Q, Cockayne syndrome (ClinVar).

How common is ERCC4 c.2017+19del in the general population?

ERCC4 c.2017+19del is absent from gnomAD (gnomAD).

ERCC4 c.2017+19del

Q: How is Xeroderma pigmentosum-Cockayne syndrome complex inherited?

Typically Autosomal recessive (Orphanet). A genetic counselor can assess individual risk for a family.

rs2032486702 · VCV2019146

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

xeroderma pigmentosum group F

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
Splice region	donor +19	near-intronic (+19 nt from the splice site)
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP -0.13	GERP -2.6
Non-coding constraint	Z 1.09	1 kb window · o/e 0.90 · regional · uncalibrated

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
Coding: c.2017+19del
MANE Select: NM_005236
dbSNP: rs2032486702
Type: Deletion
Location: chr16:13944854 (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

Disease context

xeroderma pigmentosum group F — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: Fanconi anemia complementation group Q Cockayne syndrome

For Xeroderma pigmentosum-Cockayne syndrome complex (Orphanet):

Inheritance: Autosomal recessive
Onset: Infancy, Neonatal

Similar variants

ERCC4 p.Arg468fs Pathogenic/Likely pathogenic ★★ same condition
ERCC4 p.Asn308fs Pathogenic/Likely pathogenic ★★ same condition
ERCC4 p.Glu628fs Pathogenic/Likely pathogenic ★★ same condition
ERCC4 p.Phe186fs Pathogenic/Likely pathogenic ★★ same condition
ERCC4 p.Thr495fs Pathogenic ★★ same condition
ERCC4 c.1905-8_1909del Likely pathogenic ★ same condition
ERCC4 p.Ala13fs Likely pathogenic ★ same condition
ERCC4 p.Arg576_Tyr577insTer 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-c-2017-plus-19del (accessed [today's date]).

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