Is ANTKMT p.Ala26Val (c.77C>T) pathogenic?

ANTKMT p.Ala26Val (c.77C>T) is classified Likely benign in ANTKMT (ClinVar, Single submitter, 1 submitter; last evaluated 2024-12-02). AlphaMissense: likely benign (0.0624); Ultra-rare (popmax 0.0175%, amr).

How common is ANTKMT p.Ala26Val (c.77C>T) in the general population?

ANTKMT p.Ala26Val (c.77C>T) is ultra-rare (popmax 0.0175%, amr) (gnomAD).

What do computational predictors say about ANTKMT p.Ala26Val (c.77C>T)?

AlphaMissense predicts likely benign (score 0.0624) — an in-silico prediction, not a clinical call.

ANTKMT p.Ala26Val

c.77C>T · VCV3401643

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0624 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0175%, amr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0624	likely benign
REVEL	0.054	moderately benign-leaning
SaProt	LLR -4.53	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	Δ0.24	donor gain · deltas
Constraint at this position
Conservation	phyloP -0.68	GERP -4, phastCons 0.047
Regional constraint	o/e 1.28	unconstrained · MANE · 1,279 bp · p 3.5e-07 · regional, not allelic
Overall
CADD	1.834	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 0.0175% Admixed American · 5/28,624 alleles

Filtering AF 0.00685% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00439%

Overall 0.000374% 5/1,338,476 alleles · ultra-rare exomes 4/1,186,664 · genomes 1/151,812 · joint denominator

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: ANTKMT
Protein: p.Ala26Val
Coding: c.77C>T
MANE Select: NM_023933
Type: single nucleotide variant
Location: chr16:721351 (GRCh38)
Gene constraint: LOEUF 1.948 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 82.01

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

Similar variants

ANTKMT p.Ala169Thr Uncertain significance ★ ⚠ same type
ANTKMT p.Ala196Ser Uncertain significance ★ ⚠ same type
ANTKMT p.Ala209Ser Uncertain significance ★ ⚠ same type
ANTKMT p.Ala224Asp Uncertain significance ★ ⚠ same type
ANTKMT p.Ala224Ser Uncertain significance ★ ⚠ same type
ANTKMT p.Ala36Thr Uncertain significance ★ ⚠ same type
ANTKMT p.Ala62Ser Uncertain significance ★ ⚠ same type
ANTKMT p.Ala92Val 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/antkmt-p-ala26val (accessed [today's date]).

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