Is CSRP3 p.His19fs (c.55del) pathogenic?

CSRP3 p.His19fs (c.55del) is classified Pathogenic in CSRP3 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-04-22). Absent from gnomAD; Associated with hypertrophic cardiomyopathy 12.

What condition is associated with CSRP3 p.His19fs (c.55del)?

CSRP3 p.His19fs (c.55del) is associated with hypertrophic cardiomyopathy 12, dilated cardiomyopathy 1M (ClinVar).

How common is CSRP3 p.His19fs (c.55del) in the general population?

CSRP3 p.His19fs (c.55del) is absent from gnomAD (gnomAD).

CSRP3 p.His19fs

c.55del · rs1554968138 · VCV543041

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

Conditions

hypertrophic cardiomyopathy 12

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 2 of 6
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 7.8	GERP 6.8, phastCons 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: CSRP3
Protein: p.His19fs
Coding: c.55del
MANE Select: NM_003476
dbSNP: rs1554968138
Type: Deletion
Location: chr11:19192394 (GRCh38)
Gene constraint: LOEUF 1.307 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 73.91 · 2 PDB
Residue 19: the lim zinc-binding 1 domain; an α-helix

Full CSRP3 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

hypertrophic cardiomyopathy 12 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: dilated cardiomyopathy 1M

Similar variants

CSRP3 p.His19Asp Uncertain significance ★ ⚠ same residue
CSRP3 p.Arg100fs Pathogenic ★ same condition
CSRP3 p.Arg28fs Pathogenic ★ same condition
CSRP3 p.Gln93fs Pathogenic ★ same condition
CSRP3 p.Ile56fs Pathogenic ★ same condition
CSRP3 p.Lys9fs Pathogenic ★ same condition
CSRP3 p.Val102fs Pathogenic ★ same condition
CSRP3 p.Val17fs 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/csrp3-p-his19fs (accessed [today's date]).

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