Is MID1 p.Ala34Asp (c.101C>A) pathogenic?

MID1 p.Ala34Asp (c.101C>A) is classified Uncertain significance in MID1 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-01-23). AlphaMissense: likely pathogenic (0.9999); Absent from gnomAD v4.1; Associated with MID1-related disorder.

What condition is associated with MID1 p.Ala34Asp (c.101C>A)?

MID1 p.Ala34Asp (c.101C>A) is associated with MID1-related disorder (ClinVar).

How common is MID1 p.Ala34Asp (c.101C>A) in the general population?

MID1 p.Ala34Asp (c.101C>A) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about MID1 p.Ala34Asp (c.101C>A)?

AlphaMissense predicts likely pathogenic (score 0.9999) — an in-silico prediction, not a clinical call.

MID1 p.Ala34Asp

c.101C>A · rs1366033152 · VCV2630627

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.9999 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

2/2 damaging

AlphaMissense, SaProt · REVEL indeterminate

Conditions

MID1-related disorder

Computational evidence

Protein change
AlphaMissense	0.9999	likely pathogenic · top 4% in MID1
REVEL	0.606	indeterminate
SaProt	LLR -12.13	damaging
⇒ AlphaMissense and SaProt both call this damaging; REVEL is indeterminate.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 12	GERP 2.4, phastCons 1
Regional constraint	o/e 0.69	unconstrained · MANE · 372 bp · p 0.0011 · regional, not allelic
Overall
CADD	27.0	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean damaging — 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: MID1
Protein: p.Ala34Asp
Coding: c.101C>A
MANE Select: NM_000381
dbSNP: rs1366033152
Type: single nucleotide variant
Location: chrX:10567447 (GRCh38)
Structure: AlphaFold pLDDT 86.51 · 5 PDB

Full MID1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

MID1-related disorder

Similar variants

MID1 p.Ala34= Likely benign ★ same residue
MID1 p.Ala34Thr Benign ★ ⚠ same residue
MID1 p.Gln454Ter Likely pathogenic ★ same condition
MID1 p.Asp191Asn Uncertain significance ★ ⚠ same condition
MID1 c.757-10784C>T Uncertain significance same condition
MID1 c.757-5727G>A Uncertain significance same condition
MID1 p.Leu292Pro Uncertain significance ⚠ same condition
MID1 c.757-10802C>T Likely benign 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/mid1-p-ala34asp (accessed [today's date]).

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