Is CSRP3 p.Ala50= (c.150G>A) pathogenic?

CSRP3 p.Ala50= (c.150G>A) is classified Benign/Likely benign in CSRP3 (ClinVar, Multiple submitters, 13 submitters; last evaluated 2026-02-04). Common (popmax 10.6%, afr) — too common for a highly-penetrant pathogenic allele; Associated with hypertrophic cardiomyopathy 12.

What condition is associated with CSRP3 p.Ala50= (c.150G>A)?

CSRP3 p.Ala50= (c.150G>A) is associated with hypertrophic cardiomyopathy 12, dilated cardiomyopathy 1M (ClinVar).

CSRP3 p.Ala50=

Q: How common is CSRP3 p.Ala50= (c.150G>A) in the general population?

CSRP3 p.Ala50= (c.150G>A) is common (popmax 10.6%, afr) — too common for a highly-penetrant pathogenic allele (gnomAD).

c.150G>A · rs7124801 · VCV44688

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 13 submitters

gnomAD v4.1

Common

common (popmax 10.6%, afr) — too common for a highly-penetrant pathogenic allele

Conditions

hypertrophic cardiomyopathy 12

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 -5.8	GERP -14
Overall
CADD	0.129	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 10.6% African / African-American · 7,923/74,922 alleles

Filtering AF 10.4% ClinGen BA1/BS1 input FAF95, joint · FAF99 10.3%

Overall 0.554% 8,936/1,612,710 alleles · common

Ancestry group	Frequency	1 in
African / African-Americangrpmax	10.6%	9
Remaining individualsnot grpmax-eligible	0.66%	151
Admixed American	0.595%	168
Middle Eastern	0.402%	249
European (non-Finnish)	0.0175%	5,728
South Asian	0.0165%	6,067
East Asian	0.00446%	22,438
Ashkenazi Jewishnot grpmax-eligible	0.00338%	29,602

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: CSRP3
Protein: p.Ala50=
Coding: c.150G>A
MANE Select: NM_003476
dbSNP: rs7124801
Type: single nucleotide variant
Location: chr11:19188267 (GRCh38)
Gene constraint: LOEUF 1.307 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 73.91 · 2 PDB
Residue 50: the lim zinc-binding 1 domain; a β-strand

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.Ala50Glu Uncertain significance ★★ ⚠ same residue
CSRP3 p.Ala50Thr Uncertain significance ★★ ⚠ same residue
CSRP3 p.Ala50Val Uncertain significance ★★ ⚠ same residue
CSRP3 c.414+1G>T Likely pathogenic ★★ same condition
CSRP3 p.Cys37Ter Pathogenic/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

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-ala50 (accessed [today's date]).

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