Is MYBPC3 p.Pro1069= (c.3207C>T) pathogenic?

MYBPC3 p.Pro1069= (c.3207C>T) is classified Likely benign in MYBPC3 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-04-16). No allele count reported in gnomAD v4.1 (AN 1,582,538); Associated with Cardiovascular phenotype.

What condition is associated with MYBPC3 p.Pro1069= (c.3207C>T)?

MYBPC3 p.Pro1069= (c.3207C>T) is associated with Cardiovascular phenotype (ClinVar).

How common is MYBPC3 p.Pro1069= (c.3207C>T) in the general population?

MYBPC3 p.Pro1069= (c.3207C>T) is no allele count reported in gnomAD v4.1 (AN 1,582,538) (gnomAD).

MYBPC3 p.Pro1069=

c.3207C>T · rs2495740500 · VCV2563088

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,582,538)

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 1.7	GERP -3.7, phastCons 1
Overall
CADD	6.681	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,582,538). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: MYBPC3
Protein: p.Pro1069=
Coding: c.3207C>T
MANE Select: NM_000256
dbSNP: rs2495740500
Type: single nucleotide variant
Location: chr11:47333317 (GRCh38)
Gene constraint: LOEUF 0.915 · pLI <0.01 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 79.43 · 17 PDB
Residue 1069: the fibronectin type-iii 3 domain

Full MYBPC3 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

MYBPC3 p.Pro1069Leu Uncertain significance ★ ⚠ same residue
MYBPC3 p.Pro1069Ser Uncertain significance ★ ⚠ same residue
MYBPC3 c.1090+1G>A Pathogenic ★★ same condition
MYBPC3 c.1091-2A>G Pathogenic/Likely pathogenic ★★ same condition
MYBPC3 c.1224-2A>G Pathogenic/Likely pathogenic ★★ same condition
MYBPC3 c.1224-80G>A Pathogenic/Likely pathogenic ★★ same condition
MYBPC3 c.1227-2A>G Pathogenic/Likely pathogenic ★★ same condition
MYBPC3 c.1351+1G>A Pathogenic ★★ 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/mybpc3-p-pro1069 (accessed [today's date]).

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