Is MTAP p.Ala76Val (c.227C>T) pathogenic?

MTAP p.Ala76Val (c.227C>T) is classified Uncertain significance in MTAP (ClinVar, Single submitter, 1 submitter; last evaluated 2021-10-26). AlphaMissense: likely pathogenic (0.9671); Very rare (popmax 0.00246%, nfe).

How common is MTAP p.Ala76Val (c.227C>T) in the general population?

MTAP p.Ala76Val (c.227C>T) is very rare (popmax 0.00246%, nfe) (gnomAD).

What do computational predictors say about MTAP p.Ala76Val (c.227C>T)?

AlphaMissense predicts likely pathogenic (score 0.9671) — an in-silico prediction, not a clinical call.

MTAP p.Ala76Val

c.227C>T · rs751881433 · VCV2257112

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.9671 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00246%, nfe)

Missense predictors

3/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.9671	likely pathogenic · top 9% in MTAP
REVEL	0.874	moderately pathogenic-leaning
SaProt	LLR -14.30	damaging
⇒ AlphaMissense, REVEL and SaProt all call this damaging.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.7	GERP 1.8, phastCons 1
Regional constraint	o/e 1.02	unconstrained · MANE · 59 kb · p 0.71 · regional, not allelic
Overall
CADD	33.0	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

Grpmax group 0.00246% European (non-Finnish) · 29/1,179,818 alleles

Filtering AF 0.00172% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00149%

Overall 0.00233% 34/1,461,364 alleles · very rare

Ancestry group	Frequency	1 in
Finnishnot grpmax-eligible	0.00625%	15,999
European (non-Finnish)grpmax	0.00246%	40,683
South Asian	0.0011%	90,898

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: MTAP
Protein: p.Ala76Val
Coding: c.227C>T
MANE Select: NM_002451
dbSNP: rs751881433
Type: single nucleotide variant
Location: chr9:21818082 (GRCh38)
Gene constraint: LOEUF 1.489 · pLI <0.01 · ClinGen HI 1/3 (gnomAD)
Structure: AlphaFold pLDDT 92.99 · 18 PDB
Residue 76: an α-helix

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

Similar variants

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
MTAP c.121-76T>C 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-ala76val (accessed [today's date]).

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