Is CAPN5 p.Asp10= (c.30C>T) pathogenic?

CAPN5 p.Asp10= (c.30C>T) is classified Likely benign in CAPN5 (ClinVar, Single submitter, 1 submitter; last evaluated 2021-12-30). Ultra-rare (popmax 0.0329%, sas).

How common is CAPN5 p.Asp10= (c.30C>T) in the general population?

CAPN5 p.Asp10= (c.30C>T) is ultra-rare (popmax 0.0329%, sas) (gnomAD).

CAPN5 p.Asp10=

c.30C>T · rs34801837 · VCV1918022

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0329%, sas)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.42	GERP -3.2, phastCons 0.99
Overall
CADD	8.049	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0329% South Asian · 30/91,082 alleles

Filtering AF 0.0237% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0205%

Overall 0.00223% 36/1,613,924 alleles · ultra-rare

Ancestry group	Frequency	1 in
South Asiangrpmax	0.0329%	3,036
Remaining individualsnot grpmax-eligible	0.0064%	15,621
East Asian	0.00223%	44,894
African / African-American	0.00133%	74,910

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: CAPN5
Protein: p.Asp10=
Coding: c.30C>T
MANE Select: NM_004055
dbSNP: rs34801837
Type: single nucleotide variant
Location: chr11:77084916 (GRCh38)
Gene constraint: LOEUF 0.928 · pLI <0.01 · ClinGen HI 0/3 (gnomAD)
Structure: AlphaFold pLDDT 91.71 · 1 PDB
Residue 10: an α-helix

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

Similar variants

CAPN5 p.Asp10Glu Benign/Likely benign ★★ same residue
CAPN5 p.Asp10Asn Uncertain significance ★ ⚠ same residue
CAPN5 p.Asp10Gly Uncertain significance ★ ⚠ same residue
CAPN5 p.Asp10Tyr Uncertain significance ★ ⚠ same residue
HTRA3 p.Ala10Pro Uncertain significance ★ ⚠ same residue
CAPN5 p.Arg243Leu Pathogenic ★★ ⚠ same type
CAPN5 p.Arg289Trp Pathogenic ★★ ⚠ same type
CAPN5 p.Ala118Val 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-asp10 (accessed [today's date]).

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