MYPN p.Phe342=
c.1026T>C · VCV4733123
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.000169%, nfe)
Conditions
1
dilated cardiomyopathy 1KK
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 1.9 | GERP -1.9, phastCons 1 |
| Overall | ||
| CADD | 9.409 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000169%
European (non-Finnish) · 2/1,180,018 alleles
Filtering AF
2.8e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.1e-05%
Overall
0.000124%
2/1,614,176 alleles · very rare
exomes 2/1,461,842 · genomes 0/152,334 · joint denominator
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.Phe342=
- Coding
- c.1026T>C
- MANE Select
- NM_032578
- Type
- single nucleotide variant
- Location
- chr10:68143063 (GRCh38)
- Gene constraint
- LOEUF 0.596 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 52.71
- Residue 342
- the ig-like 1 domain; the 'interaction with carp' region
Similar variants
- 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
- MYPN c.3159-3T>C 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-phe342 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown