Is MYPN p.Ser613= (c.1839C>T) pathogenic?

MYPN p.Ser613= (c.1839C>T) is classified Likely benign in MYPN (ClinVar, Multiple submitters, 3 submitters; last evaluated 2025-10-26). Ultra-rare (popmax 0.0107%, afr); Associated with Cardiovascular phenotype.

What condition is associated with MYPN p.Ser613= (c.1839C>T)?

MYPN p.Ser613= (c.1839C>T) is associated with Cardiovascular phenotype, dilated cardiomyopathy 1KK (ClinVar).

How common is MYPN p.Ser613= (c.1839C>T) in the general population?

MYPN p.Ser613= (c.1839C>T) is ultra-rare (popmax 0.0107%, afr) (gnomAD).

MYPN p.Ser613=

c.1839C>T · rs140063470 · VCV702536

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.0107%, afr)

Conditions

Cardiovascular phenotype

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 -6.1	GERP -5.3
Overall
CADD	0.294	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0107% African / African-American · 8/74,892 alleles

Filtering AF 0.00528% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00381%

Overall 0.00242% 39/1,613,994 alleles · ultra-rare exomes 31/1,461,884 · genomes 8/152,110 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.0107%	9,362
Ashkenazi Jewishnot grpmax-eligible	0.00338%	29,604
European (non-Finnish)	0.00237%	42,144
Remaining individualsnot grpmax-eligible	0.0016%	62,488
South Asian	0.0011%	91,078

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: MYPN
Protein: p.Ser613=
Coding: c.1839C>T
MANE Select: NM_032578
dbSNP: rs140063470
Type: single nucleotide variant
Location: chr10:68166532 (GRCh38)
Gene constraint: LOEUF 0.596 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 52.71
Residue 613: the 'disordered' region

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

Disease context

Cardiovascular phenotype — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: dilated cardiomyopathy 1KK

Similar variants

MYPN p.Ser613Phe Uncertain significance ★ ⚠ same residue
MYPN c.1317+1G>A Likely pathogenic ★★ same condition
MYPN p.Arg1072Ter Pathogenic ★★ same condition
MYPN p.Arg489Ter Pathogenic ★★ same condition
MYPN p.Arg996Ter Pathogenic/Likely pathogenic ★★ same condition
MYPN c.1130+3A>C Uncertain significance ★★ same condition
MYPN c.1974-3C>T Uncertain significance ★★ same condition
MYPN c.3158+6G>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/mypn-p-ser613 (accessed [today's date]).

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