Is WRN p.Lys1237fs (c.3711del) pathogenic?

WRN p.Lys1237fs (c.3711del) is classified Pathogenic/Likely pathogenic in WRN (ClinVar, Multiple submitters, 2 submitters; last evaluated 2024-04-05). No gnomAD frequency available for this variant; Associated with Werner syndrome.

What condition is associated with WRN p.Lys1237fs (c.3711del)?

WRN p.Lys1237fs (c.3711del) is associated with Werner syndrome (ClinVar).

How common is WRN p.Lys1237fs (c.3711del) in the general population?

WRN p.Lys1237fs (c.3711del) is no gnomAD frequency available for this variant (gnomAD).

How is Werner syndrome inherited?

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

WRN p.Lys1237fs

c.3711del · rs1563385391 · VCV577673

Pathogenic/Likely pathogenic Multiple submitters

Classification

Pathogenic/Likely pathogenic

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

Werner syndrome

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 32 of 35
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP -0.12	GERP -2.1

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: WRN
Protein: p.Lys1237fs
Coding: c.3711del
MANE Select: NM_000553
dbSNP: rs1563385391
Type: Deletion
Location: chr8:31154644 (GRCh38)
Gene constraint: LOEUF 0.9 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 68.75 · 51 PDB

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

Disease context

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

For Werner syndrome (Orphanet):

Inheritance: Autosomal recessive
Onset: Adolescent, Adult
Prevalence: 1-9 / 1 000 000 (Europe)

Similar variants

WRN c.2449-3_2449-2del Likely pathogenic ★★ same condition
WRN c.3381_3383+76del Likely pathogenic ★★ same condition
WRN p.Arg389fs Pathogenic/Likely pathogenic ★★ same condition
WRN p.Asn1197fs Pathogenic/Likely pathogenic ★★ same condition
WRN p.Asn1370fs Likely pathogenic ★★ same condition
WRN p.Asp163fs Pathogenic/Likely pathogenic ★★ same condition
WRN p.Asp287fs Pathogenic/Likely pathogenic ★★ same condition
WRN p.Cys646_Ser647insTer 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/wrn-p-lys1237fs (accessed [today's date]).

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