Is MSN p.Ala361Val (c.1082C>T) pathogenic?

MSN p.Ala361Val (c.1082C>T) is classified Uncertain significance in MSN (ClinVar, Single submitter, 1 submitter; last evaluated 2024-12-12). AlphaMissense: ambiguous (0.4967); Absent from gnomAD v4.1; Associated with Inborn genetic diseases.

What condition is associated with MSN p.Ala361Val (c.1082C>T)?

MSN p.Ala361Val (c.1082C>T) is associated with Inborn genetic diseases (ClinVar).

How common is MSN p.Ala361Val (c.1082C>T) in the general population?

MSN p.Ala361Val (c.1082C>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about MSN p.Ala361Val (c.1082C>T)?

AlphaMissense predicts ambiguous (score 0.4967) — an in-silico prediction, not a clinical call.

MSN p.Ala361Val

c.1082C>T · VCV3875142

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

ambiguous

0.4967 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.4967	ambiguous
REVEL	0.421	indeterminate
SaProt	LLR -5.96	tolerated
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.6	GERP 1.6, phastCons 1
Regional constraint	o/e 0.92	unconstrained · MANE · 1,730 bp · p 0.47 · regional, not allelic
Overall
CADD	24.3	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: MSN
Protein: p.Ala361Val
Coding: c.1082C>T
MANE Select: NM_002444
Type: single nucleotide variant
Location: chrX:65736917 (GRCh38)
Structure: AlphaFold pLDDT 86.77 · 10 PDB

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

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

MSN p.Arg295His Uncertain significance ★★ ⚠ same condition
MSN p.Arg393His Uncertain significance ★★ ⚠ same condition
MSN p.Ile340Thr Uncertain significance ★★ ⚠ same condition
MSN p.Pro272Leu Uncertain significance ★★ ⚠ same condition
MSN p.Pro272Ser Uncertain significance ★★ ⚠ same condition
MSN p.Ser144Cys Uncertain significance ★★ ⚠ same condition
MSN p.Thr369Ser Uncertain significance ★★ ⚠ same condition
MSN p.Tyr85Cys 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/msn-p-ala361val (accessed [today's date]).

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