Is MTAP p.Arg29Thr (c.86G>C) pathogenic?

MTAP p.Arg29Thr (c.86G>C) is classified Uncertain significance in MTAP (ClinVar, Single submitter, 1 submitter; last evaluated 2025-09-22). AlphaMissense: ambiguous (0.4187); Absent from gnomAD v4.1.

How common is MTAP p.Arg29Thr (c.86G>C) in the general population?

MTAP p.Arg29Thr (c.86G>C) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about MTAP p.Arg29Thr (c.86G>C)?

AlphaMissense predicts ambiguous (score 0.4187) — an in-silico prediction, not a clinical call.

MTAP p.Arg29Thr

c.86G>C · VCV4553673

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

ambiguous

0.4187 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

1/2 damaging

REVEL, SaProt · AlphaMissense indeterminate

Computational evidence

Protein change
AlphaMissense	0.4187	ambiguous
REVEL	0.266	benign-leaning
SaProt	LLR -11.32	damaging
⇒ SaProt calls this damaging; REVEL does not; AlphaMissense is indeterminate.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 12	GERP 1.8, phastCons 1
Regional constraint	o/e 1.02	unconstrained · MANE · 59 kb · p 0.71 · regional, not allelic
Overall
CADD	26.6	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: MTAP
Protein: p.Arg29Thr
Coding: c.86G>C
MANE Select: NM_002451
Type: single nucleotide variant
Location: chr9:21815485 (GRCh38)
Gene constraint: LOEUF 1.489 · pLI <0.01 · ClinGen HI 1/3 (gnomAD)
Structure: AlphaFold pLDDT 92.99 · 18 PDB
Residue 29: a β-strand

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

Similar variants

MTAP p.Arg29Lys Uncertain significance ★ ⚠ same residue
MTAP c.*1453C>T Uncertain significance ★★ same type
MTAP p.Gln75Arg Uncertain significance ★★ ⚠ same type
MTAP c.120+279C>T Benign ★★ same type
MTAP c.121-10T>C Benign ★★ same type
MTAP c.121-140G>A Benign ★★ same type
MTAP c.121-185A>G Benign ★★ same type
MTAP c.121-67A>G Benign ★★ 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/mtap-p-arg29thr (accessed [today's date]).

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