Is CSRP3 p.Cys37Ter (c.111C>A) pathogenic?

CSRP3 p.Cys37Ter (c.111C>A) is classified Pathogenic/Likely pathogenic in CSRP3 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2023-07-21). Absent from gnomAD v4.1; Associated with hypertrophic cardiomyopathy 12.

What condition is associated with CSRP3 p.Cys37Ter (c.111C>A)?

CSRP3 p.Cys37Ter (c.111C>A) is associated with hypertrophic cardiomyopathy 12, cardiomyopathy, dilated cardiomyopathy 1M (ClinVar).

How common is CSRP3 p.Cys37Ter (c.111C>A) in the general population?

CSRP3 p.Cys37Ter (c.111C>A) is absent from gnomAD v4.1 (gnomAD).

CSRP3 p.Cys37Ter

c.111C>A · rs1850628800 · VCV915721

Pathogenic/Likely pathogenic Multiple submitters

Classification

Pathogenic/Likely pathogenic

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

Consequence

nonsense (stop-gain)

predicted LoF

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,611,762)

Conditions

hypertrophic cardiomyopathy 12

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	nonsense (stop-gain)	predicted loss-of-function
NMD	predicted	premature termination codon in exon 2 of 6
Splicing
SpliceAI	<0.2	all four deltas below 0.2 · G>A here scores Δ0.28 · evaluated, not missing
Constraint at this position
Conservation	phyloP 8.6	GERP 6.8, phastCons 1
Overall
CADD	42.0	PHRED · no single calibrated threshold — expert panels disagree

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,611,762). 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.Cys37Ter
Coding: c.111C>A
MANE Select: NM_003476
dbSNP: rs1850628800
Type: single nucleotide variant
Location: chr11:19192338 (GRCh38)
Gene constraint: LOEUF 1.307 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 73.91 · 2 PDB
Residue 37: the lim zinc-binding 1 domain

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: cardiomyopathy dilated cardiomyopathy 1M

Similar variants

CSRP3 p.Cys37Arg Uncertain significance ★★ ⚠ same residue
CSRP3 p.Cys37Gly Uncertain significance ★ ⚠ same residue
CSRP3 c.414+1G>T Likely pathogenic ★★ same condition
CSRP3 p.Cys58Gly Pathogenic ★★ same condition
CSRP3 p.Lys113Ter Pathogenic ★★ same condition
CSRP3 c.113-3C>T Uncertain significance ★★ same condition
CSRP3 c.414+6A>G Uncertain significance ★★ same condition
CSRP3 c.415-1G>A Uncertain significance ★★ 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-cys37ter (accessed [today's date]).

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