Is CAMKMT p.Val115Phe (c.343G>T) pathogenic?

CAMKMT p.Val115Phe (c.343G>T) is classified Uncertain significance in CAMKMT (ClinVar, Single submitter, 1 submitter; last evaluated 2022-06-24). AlphaMissense: ambiguous (0.359); Very rare (popmax 0.00669%, afr).

How common is CAMKMT p.Val115Phe (c.343G>T) in the general population?

CAMKMT p.Val115Phe (c.343G>T) is very rare (popmax 0.00669%, afr) (gnomAD).

What do computational predictors say about CAMKMT p.Val115Phe (c.343G>T)?

AlphaMissense predicts ambiguous (score 0.359) — an in-silico prediction, not a clinical call.

CAMKMT p.Val115Phe

c.343G>T · rs374314875 · VCV2296630

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

ambiguous

0.359 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00669%, afr)

Missense predictors

0/2 damaging

REVEL, SaProt · AlphaMissense no call

Computational evidence

Protein change
AlphaMissense	0.359	ambiguous
REVEL	0.22	benign-leaning
SaProt	LLR -7.50	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 8.5	GERP 1.6, phastCons 1
Regional constraint	o/e 1.06	unconstrained · MANE · 410 kb · p 0.21 · regional, not allelic
Overall
CADD	25.2	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 0.00669% African / African-American · 5/74,744 alleles

Filtering AF 0.00255% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00162%

Overall 0.000373% 6/1,609,964 alleles · very rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.00669%	14,949
European (non-Finnish)	8.49e-05%	1,178,332

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: CAMKMT
Protein: p.Val115Phe
Coding: c.343G>T
MANE Select: NM_024766
dbSNP: rs374314875
Type: single nucleotide variant
Location: chr2:44390272 (GRCh38)
Gene constraint: LOEUF 1.643 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 85.97 · 1 PDB
Residue 115: an α-helix

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

Similar variants

CAMKMT p.Ile282= Benign ★★ same type
CAMKMT p.Ala16Thr Uncertain significance ★ ⚠ same type
CAMKMT p.Ala183Thr Uncertain significance ★ ⚠ same type
CAMKMT p.Ala22Ser Uncertain significance ★ ⚠ same type
CAMKMT p.Ala34Glu Uncertain significance ★ ⚠ same type
CAMKMT p.Ala38Gly Uncertain significance ★ ⚠ same type
CAMKMT p.Arg211Gln Uncertain significance ★ ⚠ same type
CAMKMT p.Arg40Gly 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/camkmt-p-val115phe (accessed [today's date]).

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