Is CSRP3 p.Gly72= (c.216G>A) pathogenic?

CSRP3 p.Gly72= (c.216G>A) is classified Likely benign in CSRP3 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-02-16). Very rare (popmax 0.005%, amr); Associated with Cardiovascular phenotype.

What condition is associated with CSRP3 p.Gly72= (c.216G>A)?

CSRP3 p.Gly72= (c.216G>A) is associated with Cardiovascular phenotype (ClinVar).

How common is CSRP3 p.Gly72= (c.216G>A) in the general population?

CSRP3 p.Gly72= (c.216G>A) is very rare (popmax 0.005%, amr) (gnomAD).

CSRP3 p.Gly72=

c.216G>A · rs751348376 · VCV3223381

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.005%, amr)

Conditions

Cardiovascular phenotype

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 -1.1	GERP -0.89, phastCons 0.001
Overall
CADD	5.807	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.005% Admixed American · 3/60,028 alleles

Filtering AF 0.00133% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000668%

Overall 0.000411% 6/1,461,588 alleles · very rare

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.005%	20,009
South Asian	0.0011%	91,062
European (non-Finnish)	0.000169%	590,016

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.Gly72=
Coding: c.216G>A
MANE Select: NM_003476
dbSNP: rs751348376
Type: single nucleotide variant
Location: chr11:19188201 (GRCh38)
Gene constraint: LOEUF 1.307 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 73.91 · 2 PDB
Residue 72: a UniProt-annotated variant site (in cmd1m; uncertain significance; increases pkc/prkca activity)

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

Disease context

Cardiovascular phenotype — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

CSRP3 p.Gly72Arg Uncertain significance ★★ ⚠ same residue
CSRP3 p.Gly72Trp Uncertain significance ★ ⚠ same residue
CSRP3 c.414+1G>T Likely pathogenic ★★ same condition
CSRP3 p.Cys58Gly Pathogenic ★★ same condition
CSRP3 c.415-1G>A Uncertain significance ★★ same condition
CSRP3 p.Ala148Val Uncertain significance ★★ ⚠ same condition
CSRP3 p.Ala173Val Uncertain significance ★★ ⚠ same condition
CSRP3 p.Ala39Asp 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-gly72 (accessed [today's date]).

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