Is CSRP3 p.Thr82Arg (c.245C>G) pathogenic?

CSRP3 p.Thr82Arg (c.245C>G) is classified Uncertain significance in CSRP3 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-07-06). AlphaMissense: likely pathogenic (0.8083); Absent from gnomAD v4.1; Associated with Cardiovascular phenotype.

What condition is associated with CSRP3 p.Thr82Arg (c.245C>G)?

CSRP3 p.Thr82Arg (c.245C>G) is associated with Cardiovascular phenotype (ClinVar).

How common is CSRP3 p.Thr82Arg (c.245C>G) in the general population?

CSRP3 p.Thr82Arg (c.245C>G) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about CSRP3 p.Thr82Arg (c.245C>G)?

AlphaMissense predicts likely pathogenic (score 0.8083) — an in-silico prediction, not a clinical call.

CSRP3 p.Thr82Arg

c.245C>G · VCV3497946

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.8083 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

2/2 damaging

AlphaMissense, SaProt · REVEL no call

Conditions

Cardiovascular phenotype

Computational evidence

Protein change
AlphaMissense	0.8083	likely pathogenic
REVEL	0.587	indeterminate
SaProt	LLR -10.51	damaging
⇒ AlphaMissense and SaProt both call this damaging; REVEL makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 8.6	GERP 4.8, phastCons 1
Regional constraint	o/e 0.96	unconstrained · MANE · 9,775 bp · p 0.57 · regional, not allelic
Overall
CADD	24.7	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean damaging — a triage signal, not a reclassification

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: CSRP3
Protein: p.Thr82Arg
Coding: c.245C>G
MANE Select: NM_003476
Type: single nucleotide variant
Location: chr11:19188172 (GRCh38)
Gene constraint: LOEUF 1.307 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 73.91 · 2 PDB

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.Thr82= Likely benign ★ 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
CSRP3 p.Ala50Thr 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-thr82arg (accessed [today's date]).

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