Is CSRP3 p.Val170Phe (c.508G>T) pathogenic?

CSRP3 p.Val170Phe (c.508G>T) is classified Uncertain significance in CSRP3 (ClinVar, Single submitter, 1 submitter; last evaluated 2014-10-20). AlphaMissense: ambiguous (0.4847); Absent from gnomAD v4.1.

How common is CSRP3 p.Val170Phe (c.508G>T) in the general population?

CSRP3 p.Val170Phe (c.508G>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about CSRP3 p.Val170Phe (c.508G>T)?

AlphaMissense predicts ambiguous (score 0.4847) — an in-silico prediction, not a clinical call.

CSRP3 p.Val170Phe

c.508G>T · rs757433657 · VCV201696

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

ambiguous

0.4847 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

1/2 damaging

REVEL, SaProt · AlphaMissense no call

Computational evidence

Protein change
AlphaMissense	0.4847	ambiguous
REVEL	0.676	pathogenic-leaning
SaProt	LLR -9.10	tolerated
⇒ REVEL calls this damaging; SaProt does not; AlphaMissense makes no call.
Splicing
SpliceAI	Δ0.24	donor loss at this position · masked 0 · deltas
Constraint at this position
Conservation	phyloP 7.7	phastCons 1
Regional constraint	o/e 0.96	unconstrained · MANE · 9,775 bp · p 0.57 · regional, not allelic
Overall
CADD	31.0	PHRED · no single calibrated threshold — expert panels disagree

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.Val170Phe
Coding: c.508G>T
MANE Select: NM_003476
dbSNP: rs757433657
Type: single nucleotide variant
Location: chr11:19184952 (GRCh38)
Gene constraint: LOEUF 1.307 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 73.91 · 2 PDB
Residue 170: the lim zinc-binding 2 domain; an α-helix

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

Similar variants

CSRP3 p.Val170Leu Uncertain significance ★ ⚠ same residue
CSRP3 c.414+1G>T Likely pathogenic ★★ same type
CSRP3 p.Cys37Ter Pathogenic/Likely pathogenic ★★ same type
CSRP3 p.Cys58Gly Pathogenic ★★ same type
CSRP3 p.Lys113Ter Pathogenic ★★ same type
CSRP3 c.113-3C>T Uncertain significance ★★ same type
CSRP3 c.414+6A>G Uncertain significance ★★ same type
CSRP3 c.415-1G>A Uncertain significance ★★ same type

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-val170phe (accessed [today's date]).

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