Is DMPK p.Pro554= (c.1662G>A) pathogenic?

DMPK p.Pro554= (c.1662G>A) is classified Likely benign in DMPK (ClinVar, Single submitter, 1 submitter; last evaluated 2024-03-01). Ultra-rare (popmax 0.013%, amr); Associated with Inborn genetic diseases.

What condition is associated with DMPK p.Pro554= (c.1662G>A)?

DMPK p.Pro554= (c.1662G>A) is associated with Inborn genetic diseases (ClinVar).

How common is DMPK p.Pro554= (c.1662G>A) in the general population?

DMPK p.Pro554= (c.1662G>A) is ultra-rare (popmax 0.013%, amr) (gnomAD).

DMPK p.Pro554=

c.1662G>A · rs956079556 · VCV3083101

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.013%, amr)

Conditions

Inborn genetic diseases

⚠ Built without this gene's context — gene constraint and dosage, protein structure, pathways, panels and related-variant links were not looked up for this page. why

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.308	indeterminate
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP 5.8	GERP 1.5, phastCons 1
Overall
CADD	15.69	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.013% Admixed American · 6/46,254 alleles

Filtering AF 0.00565% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00385%

Overall 0.00125% 19/1,515,582 alleles · ultra-rare exomes 16/1,363,394 · genomes 3/152,188 · joint denominator

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.013%	7,709
Remaining individualsnot grpmax-eligible	0.00854%	11,712
African / African-American	0.00845%	11,837
European (non-Finnish)	0.000176%	566,675

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: DMPK
Protein: p.Pro554=
Coding: c.1662G>A
MANE Select: NM_004409
dbSNP: rs956079556
Type: single nucleotide variant
Location: chr19:45771046 (GRCh38)

Full DMPK 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

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/dmpk-p-pro554 (accessed [today's date]).

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