Is MIPEP p.Asp653Val (c.1958A>T) pathogenic?

MIPEP p.Asp653Val (c.1958A>T) is classified Uncertain significance in MIPEP (ClinVar, Single submitter, 1 submitter; last evaluated 2022-10-26). AlphaMissense: ambiguous (0.3883); Absent from gnomAD v4.1; Associated with Inborn genetic diseases.

What condition is associated with MIPEP p.Asp653Val (c.1958A>T)?

MIPEP p.Asp653Val (c.1958A>T) is associated with Inborn genetic diseases (ClinVar).

How common is MIPEP p.Asp653Val (c.1958A>T) in the general population?

MIPEP p.Asp653Val (c.1958A>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about MIPEP p.Asp653Val (c.1958A>T)?

AlphaMissense predicts ambiguous (score 0.3883) — an in-silico prediction, not a clinical call.

MIPEP p.Asp653Val

c.1958A>T · rs2547644879 · VCV2320872

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

ambiguous

0.3883 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.3883	ambiguous
REVEL	0.519	indeterminate
SaProt	LLR -15.55	damaging
Splicing
SpliceAI	Δ0.23	donor loss, 20 bp away · masked 0 · deltas
Constraint at this position
Conservation	phyloP 7.7	GERP 2.1, phastCons 1
Regional constraint	o/e 1.04	unconstrained · MANE · 159 kb · p 0.25 · regional, not allelic
Overall
CADD	25.7	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: MIPEP
Protein: p.Asp653Val
Coding: c.1958A>T
MANE Select: NM_005932
dbSNP: rs2547644879
Type: single nucleotide variant
Location: chr13:23760108 (GRCh38)
Gene constraint: LOEUF 1.181 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 90.33

Full MIPEP 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

MIPEP p.Ala138Val Uncertain significance ★★ ⚠ same condition
MIPEP p.Arg366Cys Uncertain significance ★★ same condition
MIPEP p.Arg453His Uncertain significance ★★ ⚠ same condition
MIPEP p.Arg509His Uncertain significance ★★ ⚠ same condition
MIPEP p.Arg560His Uncertain significance ★★ ⚠ same condition
MIPEP p.Arg621Gln Uncertain significance ★★ same condition
MIPEP p.Arg662Cys Uncertain significance ★★ ⚠ same condition
MIPEP p.Asp168Ala 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/mipep-p-asp653val (accessed [today's date]).

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