Is MYOZ2 p.Pro130= (c.390A>T) pathogenic?

MYOZ2 p.Pro130= (c.390A>T) is classified Likely benign in MYOZ2 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-07-15). Absent from gnomAD v4.1; Associated with Cardiovascular phenotype.

What condition is associated with MYOZ2 p.Pro130= (c.390A>T)?

MYOZ2 p.Pro130= (c.390A>T) is associated with Cardiovascular phenotype (ClinVar).

How common is MYOZ2 p.Pro130= (c.390A>T) in the general population?

MYOZ2 p.Pro130= (c.390A>T) is absent from gnomAD v4.1 (gnomAD).

MYOZ2 p.Pro130=

c.390A>T · rs1578738374 · VCV2626092

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

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 -0.94	GERP -3.8
Overall
CADD	7.553	PHRED · no single calibrated threshold — expert panels disagree

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: MYOZ2
Protein: p.Pro130=
Coding: c.390A>T
MANE Select: NM_016599
dbSNP: rs1578738374
Type: single nucleotide variant
Location: chr4:119164224 (GRCh38)
Gene constraint: LOEUF 1.033 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 65.51
Residue 130: the 'disordered' region

Full MYOZ2 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

Similar variants

MYOZ2 p.Pro130Leu Uncertain significance ★ ⚠ same residue
MYOZ2 c.246+4G>A Uncertain significance ★★ same condition
MYOZ2 c.560+2T>C Uncertain significance ★★ same condition
MYOZ2 c.-3A>G Uncertain significance ★★ same condition
MYOZ2 p.Ala104Val Uncertain significance ★★ ⚠ same condition
MYOZ2 p.Ala189Val Uncertain significance ★★ ⚠ same condition
MYOZ2 p.Arg115Ter Uncertain significance ★★ same condition
MYOZ2 p.Arg183Ser 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/myoz2-p-pro130 (accessed [today's date]).

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