Is ANTKMT p.Arg52Pro (c.155G>C) pathogenic?

ANTKMT p.Arg52Pro (c.155G>C) is classified Uncertain significance in ANTKMT (ClinVar, Single submitter, 1 submitter; last evaluated 2025-04-11). AlphaMissense: likely benign (0.2497); Absent from gnomAD v4.1.

How common is ANTKMT p.Arg52Pro (c.155G>C) in the general population?

ANTKMT p.Arg52Pro (c.155G>C) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about ANTKMT p.Arg52Pro (c.155G>C)?

AlphaMissense predicts likely benign (score 0.2497) — an in-silico prediction, not a clinical call.

ANTKMT p.Arg52Pro

c.155G>C · VCV3920547

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.2497 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.2497	likely benign
REVEL	0.206	benign-leaning
SaProt	LLR -9.29	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 5.3	GERP 0.69, phastCons 1
Regional constraint	o/e 1.28	unconstrained · MANE · 1,279 bp · p 3.5e-07 · regional, not allelic
Overall
CADD	26.5	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — 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

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: ANTKMT
Protein: p.Arg52Pro
Coding: c.155G>C
MANE Select: NM_023933
Type: single nucleotide variant
Location: chr16:721429 (GRCh38)
Gene constraint: LOEUF 1.948 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 82.01
Residue 52: the 'methyltransferase (mtase)' region; the 'pre-methyltransferase (premt)' region

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-arg52pro (accessed [today's date]).

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