Is CLASRP p.Ala231Val (c.692C>T) pathogenic?

CLASRP p.Ala231Val (c.692C>T) is classified Uncertain significance in CLASRP (ClinVar, Single submitter, 1 submitter; last evaluated 2025-06-07). AlphaMissense: likely benign (0.2561); Absent from gnomAD v4.1.

How common is CLASRP p.Ala231Val (c.692C>T) in the general population?

CLASRP p.Ala231Val (c.692C>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about CLASRP p.Ala231Val (c.692C>T)?

AlphaMissense predicts likely benign (score 0.2561) — an in-silico prediction, not a clinical call.

CLASRP p.Ala231Val

c.692C>T · VCV4003267

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.2561 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.2561	likely benign
REVEL	0.06	moderately benign-leaning
SaProt	LLR -5.62	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.7	GERP 2.2, phastCons 1
Regional constraint	o/e 0.70	unconstrained · MANE · 4,054 bp · p 8.8e-05 · regional, not allelic
Overall
CADD	23.0	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — 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: CLASRP
Protein: p.Ala231Val
Coding: c.692C>T
MANE Select: NM_007056
Type: single nucleotide variant
Location: chr19:45059346 (GRCh38)
Gene constraint: LOEUF 0.699 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 59.62
Residue 231: the 'disordered' region

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

Similar variants

CLASRP p.Ala157Thr Uncertain significance ★ ⚠ same type
CLASRP p.Ala346Gly Uncertain significance ★ ⚠ same type
CLASRP p.Ala371Thr Uncertain significance ★ ⚠ same type
CLASRP p.Ala415Thr Uncertain significance ★ ⚠ same type
CLASRP p.Ala545Pro Uncertain significance ★ ⚠ same type
CLASRP p.Ala549Val Uncertain significance ★ ⚠ same type
CLASRP p.Ala561Thr Uncertain significance ★ ⚠ same type
CLASRP p.Ala592Val 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/clasrp-p-ala231val (accessed [today's date]).

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