Is MIP p.Ala92Val (c.275C>T) pathogenic?

MIP p.Ala92Val (c.275C>T) is classified Uncertain significance in MIP (ClinVar, Single submitter, 1 submitter; last evaluated 2026-05-11). AlphaMissense: ambiguous (0.4297); Absent from gnomAD v4.1; Associated with Inborn genetic diseases.

What condition is associated with MIP p.Ala92Val (c.275C>T)?

MIP p.Ala92Val (c.275C>T) is associated with Inborn genetic diseases (ClinVar).

How common is MIP p.Ala92Val (c.275C>T) in the general population?

MIP p.Ala92Val (c.275C>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about MIP p.Ala92Val (c.275C>T)?

AlphaMissense predicts ambiguous (score 0.4297) — an in-silico prediction, not a clinical call.

MIP p.Ala92Val

c.275C>T · VCV4860047

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

ambiguous

0.4297 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

2/2 damaging

REVEL, SaProt · AlphaMissense indeterminate

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.4297	ambiguous
REVEL	0.912	moderately pathogenic-leaning
SaProt	LLR -12.37	damaging
⇒ REVEL and SaProt both call this damaging; AlphaMissense is indeterminate.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 12	GERP 1.7, phastCons 1
Overall
CADD	25.5	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: MIP
Protein: p.Ala92Val
Coding: c.275C>T
MANE Select: NM_012064
Type: single nucleotide variant
Location: chr12:56454339 (GRCh38)
Structure: AlphaFold pLDDT 78.91

Full MIP 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

MIP p.Glu232Gln Uncertain significance ★★ ⚠ same condition
MIP p.Gly165Ser Uncertain significance ★★ ⚠ same condition
MIP p.Lys238Thr Uncertain significance ★★ ⚠ same condition
MIP p.Val142Met Uncertain significance ★★ ⚠ same condition
MIP c.606+1G>A Conflicting classifications of pathogenicity ★ same condition
MIP p.Ala101Val Uncertain significance ★ ⚠ same condition
MIP p.Ala12Ser Uncertain significance ★ ⚠ same condition
MIP p.Ala163Asp 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/mip-p-ala92val (accessed [today's date]).

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