Is ERCC6 p.Ser1209fs (c.3623_3624insTG) pathogenic?

ERCC6 p.Ser1209fs (c.36233624insTG) is classified Likely pathogenic in ERCC6 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-05-20). Absent from gnomAD; Associated with Cockayne syndrome type 2.

What condition is associated with ERCC6 p.Ser1209fs (c.3623_3624insTG)?

ERCC6 p.Ser1209fs (c.3623_3624insTG) is associated with Cockayne syndrome type 2 (ClinVar).

How common is ERCC6 p.Ser1209fs (c.3623_3624insTG) in the general population?

ERCC6 p.Ser1209fs (c.3623_3624insTG) is absent from gnomAD (gnomAD).

How is Cockayne syndrome inherited?

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

ERCC6 p.Ser1209fs

c.3623_3624insTG · rs2495971049 · VCV1726183

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

Cockayne syndrome type 2

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 18 of 21
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 0.11	GERP -4

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: ERCC6
Protein: p.Ser1209fs
Coding: c.3623_3624insTG
MANE Select: NM_000124
dbSNP: rs2495971049
Type: Insertion
Location: chr10:49470336 (GRCh38)
Gene constraint: LOEUF 0.803 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 70.12 · 12 PDB
Residue 1209: the 'disordered' region

Full ERCC6 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Cockayne syndrome type 2 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Cockayne syndrome (Orphanet):

Inheritance: Autosomal recessive
Onset: All ages
Prevalence: 1-9 / 1 000 000 (Europe)

Similar variants

ERCC6 p.Lys1203fs Pathogenic ★★ same condition
ERCC6 p.Lys345fs Pathogenic ★★ same condition
ERCC6 p.Ala1191fs Likely pathogenic ★ same condition
ERCC6 p.Arg961fs Likely pathogenic ★ same condition
ERCC6 p.Asp425fs Likely pathogenic ★ same condition
ERCC6 p.Asp770fs Likely pathogenic ★ same condition
ERCC6 p.Glu284fs Pathogenic ★ same condition
ERCC6 p.Ile623fs 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/ercc6-p-ser1209fs (accessed [today's date]).

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