Is MYO7A p.Pro1909= (c.5727T>G) pathogenic?

MYO7A p.Pro1909= (c.5727T>G) is classified Likely benign in MYO7A (ClinVar, Multiple submitters, 2 submitters; last evaluated 2024-02-23). Absent from gnomAD v4.1.

How common is MYO7A p.Pro1909= (c.5727T>G) in the general population?

MYO7A p.Pro1909= (c.5727T>G) is absent from gnomAD v4.1 (gnomAD).

MYO7A p.Pro1909=

c.5727T>G · rs2497719754 · VCV2642180

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Absent

absent from gnomAD v4.1

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 -10	GERP -2.9
Overall
CADD	0.068	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: MYO7A
Protein: p.Pro1909=
Coding: c.5727T>G
MANE Select: NM_000260
dbSNP: rs2497719754
Type: single nucleotide variant
Location: chr11:77206187 (GRCh38)
Gene constraint: LOEUF 0.995 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 77.73 · 1 PDB
Residue 1909: the ferm 2 domain; a turn

Full MYO7A gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

MYO7A p.Pro1909Ala Uncertain significance ★ ⚠ same residue
MYO7A p.Pro1909Leu Uncertain significance ★ ⚠ same residue
MYO7A p.Pro1909fs Pathogenic ★ same residue
MYO7A p.Ala1288Pro Likely pathogenic ★★★ same type
MYO7A p.Arg1168Gln Pathogenic ★★★ ⚠ same type
MYO7A p.Arg1873Gln Pathogenic ★★★ ⚠ same type
MYO7A p.Arg395Cys Likely pathogenic ★★★ ⚠ same type
MYO7A p.Arg668Cys Pathogenic ★★★ same type

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/myo7a-p-pro1909 (accessed [today's date]).

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