Is MID2 p.Ser134Arg (c.402C>G) pathogenic?

MID2 p.Ser134Arg (c.402C>G) is classified Uncertain significance in MID2 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-04-18). AlphaMissense: ambiguous (0.4021); Very rare (popmax 0.00176%, afr).

How common is MID2 p.Ser134Arg (c.402C>G) in the general population?

MID2 p.Ser134Arg (c.402C>G) is very rare (popmax 0.00176%, afr) (gnomAD).

What do computational predictors say about MID2 p.Ser134Arg (c.402C>G)?

AlphaMissense predicts ambiguous (score 0.4021) — an in-silico prediction, not a clinical call.

MID2 p.Ser134Arg

c.402C>G · rs761567068 · VCV1683338

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

ambiguous

0.4021 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00176%, afr)

Missense predictors

0/2 damaging

REVEL, SaProt · AlphaMissense indeterminate

Computational evidence

Protein change
AlphaMissense	0.4021	ambiguous
REVEL	0.277	benign-leaning
SaProt	LLR -6.32	tolerated
⇒ REVEL and SaProt both call this tolerated; AlphaMissense is indeterminate.
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP 0.69	GERP 0.67, phastCons 1
Regional constraint	o/e 0.75	unconstrained · MANE · 101 kb · p 1.7e-09 · regional, not allelic
Overall
CADD	15.74	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 0.00176% African / African-American · 1/56,941 alleles

Filtering AF 3.7e-05% ClinGen BA1/BS1 input FAF95, joint · FAF99 1.4e-05%

Overall 0.000248% 3/1,209,458 alleles · very rare exomes 2/1,098,141 · genomes 1/111,317 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.00176%	56,941
European (non-Finnish)	0.000223%	447,573

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: MID2
Protein: p.Ser134Arg
Coding: c.402C>G
MANE Select: NM_012216
dbSNP: rs761567068
Type: single nucleotide variant
Location: chrX:107841067 (GRCh38)
Structure: AlphaFold pLDDT 80.18 · 4 PDB

Full MID2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

MID2 p.Ala150Ser Uncertain significance ★★ ⚠ same type
MID2 p.Arg121His Uncertain significance ★★ ⚠ same type
MID2 p.Arg164Gly Uncertain significance ★★ ⚠ same type
MID2 p.Ser60= Benign ★★ same type
MID2 p.Thr194= Benign/Likely benign ★★ same type
MID2 p.Arg105Pro Uncertain significance ★ ⚠ same type
MID2 p.Arg121Cys Uncertain significance ★ ⚠ same type
MID2 p.Arg121Leu 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/mid2-p-ser134arg (accessed [today's date]).

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