Is MTFMT p.Val5Met (c.13G>A) pathogenic?

MTFMT p.Val5Met (c.13G>A) is classified Uncertain significance in MTFMT (ClinVar, Single submitter, 1 submitter; last evaluated 2025-06-18). AlphaMissense: ambiguous (0.3786); No allele count reported in gnomAD v4.1 (AN 1,428,356); Associated with Inborn genetic diseases.

What condition is associated with MTFMT p.Val5Met (c.13G>A)?

MTFMT p.Val5Met (c.13G>A) is associated with Inborn genetic diseases (ClinVar).

How common is MTFMT p.Val5Met (c.13G>A) in the general population?

MTFMT p.Val5Met (c.13G>A) is no allele count reported in gnomAD v4.1 (AN 1,428,356) (gnomAD).

What do computational predictors say about MTFMT p.Val5Met (c.13G>A)?

AlphaMissense predicts ambiguous (score 0.3786) — an in-silico prediction, not a clinical call.

MTFMT p.Val5Met

c.13G>A · VCV4111706

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

ambiguous

0.3786 · ACMG-weighted

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,428,356)

Missense predictors

0/2 damaging

REVEL, SaProt · AlphaMissense no call

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.3786	ambiguous
REVEL	0.039	moderately benign-leaning
SaProt	LLR -8.40	tolerated
⇒ REVEL and SaProt both call this tolerated; AlphaMissense makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -2.8	GERP -1.2
Regional constraint	o/e 1.06	unconstrained · MANE · 27 kb · p 0.18 · regional, not allelic
Overall
CADD	10.33	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

No allele count reported in gnomAD v4.1 (AN 1,428,356). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: MTFMT
Protein: p.Val5Met
Coding: c.13G>A
MANE Select: NM_139242
Type: single nucleotide variant
Location: chr15:65029601 (GRCh38)
Gene constraint: LOEUF 1.304 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 86.08
Residue 5: a UniProt-annotated variant site (in)

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

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

MTFMT p.Val5Ala Benign ★★ same residue
MTFMT p.Val5= Likely benign ★ same residue
MTFMT p.Ala280Val Uncertain significance ★★ ⚠ same condition
MTFMT p.Ala383Gly Uncertain significance ★★ ⚠ same condition
MTFMT p.Arg154His Uncertain significance ★★ ⚠ same condition
MTFMT p.Arg21Thr Uncertain significance ★★ ⚠ same condition
MTFMT p.Arg31Pro Uncertain significance ★★ ⚠ same condition
MTFMT p.Arg371Lys Uncertain significance ★★ ⚠ 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/mtfmt-p-val5met (accessed [today's date]).

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