Is MID1 p.Arg102Gln (c.305G>A) pathogenic?

MID1 p.Arg102Gln (c.305G>A) is classified Benign in MID1 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-09-18). AlphaMissense: likely benign (0.1332); Very rare (popmax 0.00302%, nfe).

How common is MID1 p.Arg102Gln (c.305G>A) in the general population?

MID1 p.Arg102Gln (c.305G>A) is very rare (popmax 0.00302%, nfe) (gnomAD).

What do computational predictors say about MID1 p.Arg102Gln (c.305G>A)?

AlphaMissense predicts likely benign (score 0.1332) — an in-silico prediction, not a clinical call.

MID1 p.Arg102Gln

c.305G>A · rs200381037 · VCV2896990

Benign Single submitter

Classification

Benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1332 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00302%, nfe)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.1332	likely benign
REVEL	0.088	moderately benign-leaning
SaProt	LLR -6.97	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 7.6	GERP 2.4, phastCons 1
Regional constraint	o/e 0.69	unconstrained · MANE · 372 bp · p 0.0011 · regional, not allelic
Overall
CADD	24.2	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

Grpmax group 0.00302% European (non-Finnish) · 27/893,365 alleles

Filtering AF 0.00207% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00182%

Overall 0.0107% 129/1,207,162 alleles · very rare exomes 107/1,095,727 · genomes 22/111,435 · joint denominator

Ancestry group	Frequency	1 in
Finnishnot grpmax-eligible	0.205%	489
Remaining individualsnot grpmax-eligible	0.0147%	6,787
European (non-Finnish)grpmax	0.00302%	33,088

Finnish shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: MID1
Protein: p.Arg102Gln
Coding: c.305G>A
MANE Select: NM_000381
dbSNP: rs200381037
Type: single nucleotide variant
Location: chrX:10567243 (GRCh38)
Structure: AlphaFold pLDDT 86.51 · 5 PDB

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

Similar variants

MID1 p.Arg102Trp Uncertain significance ★ ⚠ same residue
MID1 p.Ala130Thr Pathogenic/Likely pathogenic ★★ same type
MID1 p.Arg277Ter Pathogenic ★★ same type
MID1 p.Arg368Ter Pathogenic ★★ same type
MID1 p.Arg495Ter Pathogenic ★★ same type
MID1 c.864+4T>G Uncertain significance ★★ same type
MID1 p.Ala114Thr Uncertain significance ★★ ⚠ same type
MID1 p.Ala211Pro 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/mid1-p-arg102gln (accessed [today's date]).

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