Is DMPK p.Ser39= (c.117C>T) pathogenic?

DMPK p.Ser39= (c.117C>T) is classified Likely benign in DMPK (ClinVar, Single submitter, 1 submitter; last evaluated 2025-03-07). Very rare (popmax 0.00806%, afr); Associated with Inborn genetic diseases.

What condition is associated with DMPK p.Ser39= (c.117C>T)?

DMPK p.Ser39= (c.117C>T) is associated with Inborn genetic diseases (ClinVar).

How common is DMPK p.Ser39= (c.117C>T) in the general population?

DMPK p.Ser39= (c.117C>T) is very rare (popmax 0.00806%, afr) (gnomAD).

DMPK p.Ser39=

c.117C>T · VCV3840519

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00806%, afr)

Conditions

Inborn genetic diseases

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.53	GERP 0.71, phastCons 0.99
Overall
CADD	15.58	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00806% African / African-American · 6/74,412 alleles

Filtering AF 0.00349% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00279%

Overall 0.00379% 61/1,608,970 alleles · very rare exomes 52/1,457,688 · genomes 9/151,282 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.00806%	12,402
East Asian	0.00449%	22,292
South Asian	0.00441%	22,652
European (non-Finnish)	0.00407%	24,550
Remaining individualsnot grpmax-eligible	0.00161%	62,290

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.Ser39=
Coding: c.117C>T
MANE Select: NM_004409
Type: single nucleotide variant
Location: chr19:45782236 (GRCh38)
Gene constraint: LOEUF 0.67 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 78.91 · 2 PDB

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

Similar variants

DMPK p.Pro257= Likely benign ★★ same condition
DMPK c.161-106C>A Uncertain significance ★ same condition
DMPK c.161-115A>G Uncertain significance ★ same condition
DMPK c.161-123A>C Uncertain significance ★ same condition
DMPK c.161-146G>A Uncertain significance ★ same condition
DMPK c.161-27G>T Uncertain significance ★ same condition
DMPK c.161-48G>C Uncertain significance ★ same condition
DMPK c.161-6C>T Uncertain significance ★ same condition

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-ser39 (accessed [today's date]).

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