Is CAPN5 p.Pro601fs (c.1802del) pathogenic?

CAPN5 p.Pro601fs (c.1802del) is classified Uncertain significance in CAPN5 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-02-22). No gnomAD frequency available for this variant.

How common is CAPN5 p.Pro601fs (c.1802del) in the general population?

CAPN5 p.Pro601fs (c.1802del) is no gnomAD frequency available for this variant (gnomAD).

CAPN5 p.Pro601fs

c.1802del · rs2496318458 · VCV2101737

Uncertain significance Single submitter

Classification

Uncertain significance

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	escapes	premature termination codon in the last exon (13 of 13) — the truncated protein is likely expressed. PVS1 input, not an applied code
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 3.6	GERP -0.22, phastCons 0.031

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: CAPN5
Protein: p.Pro601fs
Coding: c.1802del
MANE Select: NM_004055
dbSNP: rs2496318458
Type: Deletion
Location: chr11:77123747 (GRCh38)
Gene constraint: LOEUF 0.928 · pLI <0.01 · ClinGen HI 0/3 (gnomAD)
Structure: AlphaFold pLDDT 91.71 · 1 PDB
Residue 601: the c2 domain

Full CAPN5 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CAPN5 p.Pro601Leu Uncertain significance ★★ ⚠ same residue
CAPN5 p.Pro601= Likely benign ★★ same residue
CAPN5 p.Leu31fs Uncertain significance ★★ same type
CAPN5 p.Ser634_Ter641del Uncertain significance ★★ same type
CAPN5 p.Tyr41del Uncertain significance ★★ same type
CAPN5 c.971+11_971+12del Likely benign ★★ same type
CAPN5 c.165+5del Uncertain significance ★ same type
CAPN5 p.Arg62fs Uncertain significance ★ 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/capn5-p-pro601fs (accessed [today's date]).

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