Is DNMT1 p.Pro1546Ser (c.4636C>T) pathogenic?

DNMT1 p.Pro1546Ser (c.4636C>T) is classified Likely pathogenic in DNMT1 (ClinVar, Single submitter, 1 submitter; last evaluated 2021-07-12). AlphaMissense: likely pathogenic (0.9973); Absent from gnomAD v4.1; Associated with spastic ataxia.

What condition is associated with DNMT1 p.Pro1546Ser (c.4636C>T)?

DNMT1 p.Pro1546Ser (c.4636C>T) is associated with spastic ataxia (ClinVar).

How common is DNMT1 p.Pro1546Ser (c.4636C>T) in the general population?

DNMT1 p.Pro1546Ser (c.4636C>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about DNMT1 p.Pro1546Ser (c.4636C>T)?

AlphaMissense predicts likely pathogenic (score 0.9973) — an in-silico prediction, not a clinical call.

DNMT1 p.Pro1546Ser

c.4636C>T · rs1555687655 · VCV1027527

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.9973 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

3/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

spastic ataxia

Computational evidence

Protein change
AlphaMissense	0.9973	likely pathogenic ✓ concordant with ClinVar · top 6% in DNMT1
REVEL	0.737	pathogenic-leaning
SaProt	LLR -11.24	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 11	GERP 0.72, phastCons 1
Regional constraint	o/e 0.09	constrained · MANE · 117 bp · p 1.1e-11 · regional, not allelic
Overall
CADD	26.9	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

⚠ Isoform check: AlphaMissense numbered on a different transcript (AM P1530S vs ClinVar P1546S) — verify the residue.

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: DNMT1
Protein: p.Pro1546Ser
Coding: c.4636C>T
MANE Select: NM_001130823
dbSNP: rs1555687655
Type: single nucleotide variant
Location: chr19:10136141 (GRCh38)
Gene constraint: LOEUF 0.15 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 77.88 · 29 PDB
Residue 1546: the sam-dependent mtase c5-type domain; the 'interaction with the prc2/eed-ezh2 complex' region; a β-strand

Full DNMT1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

spastic ataxia — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

DNMT1 p.Pro1546= Likely benign ★★ same residue
DNMT1 p.Ala1104Val Conflicting classifications of pathogenicity ★ ⚠ same condition
DNMT1 p.Ala570Val Pathogenic ★★ ⚠ same type
DNMT1 p.Tyr511Cys Pathogenic/Likely pathogenic ★★ same type
DNMT1 c.1280+2T>C Uncertain significance ★★ same type
DNMT1 c.3524-5G>T Uncertain significance ★★ same type
DNMT1 c.494-4A>G Uncertain significance ★★ same type
DNMT1 c.*211G>C 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/dnmt1-p-pro1546ser (accessed [today's date]).

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