Is CERKL p.Pro342fs (c.1025del) pathogenic?

CERKL p.Pro342fs (c.1025del) is classified Pathogenic in CERKL (ClinVar, Single submitter, 1 submitter; last evaluated 2023-11-07). No gnomAD frequency available for this variant.

How common is CERKL p.Pro342fs (c.1025del) in the general population?

CERKL p.Pro342fs (c.1025del) is no gnomAD frequency available for this variant (gnomAD).

CERKL p.Pro342fs

c.1025del · rs2468295626 · VCV2986340

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 7 of 13
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 0.13	GERP -3.2, phastCons 0.05

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: CERKL
Protein: p.Pro342fs
Coding: c.1025del
MANE Select: NM_201548
dbSNP: rs2468295626
Type: Deletion
Location: chr2:181548728 (GRCh38)
Gene constraint: LOEUF 1.43 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 79.82

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

Similar variants

CERKL p.Pro342= Likely benign ★ same residue
CERKL c.1133+2del Likely pathogenic ★★ same type
CERKL c.237_238+13del Pathogenic/Likely pathogenic ★★ same type
CERKL c.677+562del Pathogenic/Likely pathogenic ★★ same type
CERKL p.Asn142fs Pathogenic/Likely pathogenic ★★ same type
CERKL p.Cys107_Ser108insTer Pathogenic/Likely pathogenic ★★ same type
CERKL p.Gln74fs Pathogenic/Likely pathogenic ★★ same type
CERKL p.Glu218fs 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/cerkl-p-pro342fs (accessed [today's date]).

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