Is MMUT p.Val136Phe (c.406G>T) pathogenic?

MMUT p.Val136Phe (c.406G>T) is classified Pathogenic/Likely pathogenic in MMUT (ClinVar, Multiple submitters, 2 submitters; last evaluated 2025-08-19). AlphaMissense: likely pathogenic (0.9791); Absent from gnomAD v4.1; Associated with Methylmalonic aciduria due to complete methylmalonyl-CoA mutase deficiency.

What condition is associated with MMUT p.Val136Phe (c.406G>T)?

MMUT p.Val136Phe (c.406G>T) is associated with Methylmalonic aciduria due to complete methylmalonyl-CoA mutase deficiency (ClinVar).

How common is MMUT p.Val136Phe (c.406G>T) in the general population?

MMUT p.Val136Phe (c.406G>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about MMUT p.Val136Phe (c.406G>T)?

AlphaMissense predicts likely pathogenic (score 0.9791) — an in-silico prediction, not a clinical call.

MMUT p.Val136Phe

c.406G>T · rs1767739165 · VCV1071892

Pathogenic/Likely pathogenic Multiple submitters

Classification

Pathogenic/Likely pathogenic

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

AlphaMissense

likely pathogenic

0.9791 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

3/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Methylmalonic aciduria due to complete methylmalonyl-CoA mutase deficiency

Computational evidence

Protein change
AlphaMissense	0.9791	likely pathogenic ✓ concordant with ClinVar
REVEL	0.972	strongly pathogenic-leaning
SaProt	LLR -14.15	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 4.8	GERP 1.9, phastCons 1
Regional constraint	o/e 0.94	unconstrained · MANE · 28 kb · p 0.059 · regional, not allelic
Overall
CADD	27.1	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: MMUT
Protein: p.Val136Phe
Coding: c.406G>T
MANE Select: NM_000255
dbSNP: rs1767739165
Type: single nucleotide variant
Location: chr6:49458038 (GRCh38)
Gene constraint: LOEUF 1.18 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 92.72 · 6 PDB
Residue 136: a β-strand; a UniProt-annotated variant site (in mamm; mut-)

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

Disease context

Methylmalonic aciduria due to complete methylmalonyl-CoA mutase deficiency

Similar variants

MMUT p.Val136Ile Uncertain significance ★★ ⚠ same residue
MMUT c.1084-10A>G Pathogenic/Likely pathogenic ★★ same condition
MMUT c.1445-2A>G Pathogenic/Likely pathogenic ★★ same condition
MMUT c.1560+1G>T Pathogenic ★★ same condition
MMUT c.1677-1G>A Pathogenic ★★ same condition
MMUT c.1956+2T>C Pathogenic/Likely pathogenic ★★ same condition
MMUT c.1957-2A>G Pathogenic ★★ same condition
MMUT c.2124+1G>A Pathogenic/Likely pathogenic ★★ 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/mmut-p-val136phe (accessed [today's date]).

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