Is MYO7A p.Arg920= (c.2758C>A) pathogenic?

MYO7A p.Arg920= (c.2758C>A) is classified Likely benign in MYO7A (ClinVar, Single submitter, 1 submitter; last evaluated 2024-06-13). Very rare (popmax 0.00171%, amr).

How common is MYO7A p.Arg920= (c.2758C>A) in the general population?

MYO7A p.Arg920= (c.2758C>A) is very rare (popmax 0.00171%, amr) (gnomAD).

MYO7A p.Arg920=

c.2758C>A · rs373089701 · VCV1157390

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00171%, amr)

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 7.6	GERP 1.6, phastCons 1
Overall
CADD	14.32	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00171% Admixed American · 1/58,470 alleles

Filtering AF 2.8e-05% ClinGen BA1/BS1 input FAF95, joint · FAF99 1.1e-05%

Overall 0.000187% 3/1,604,164 alleles · very rare exomes 1/1,451,958 · genomes 2/152,206 · joint denominator

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.00171%	58,470
European (non-Finnish)	0.00017%	587,927

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: MYO7A
Protein: p.Arg920=
Coding: c.2758C>A
MANE Select: NM_000260
dbSNP: rs373089701
Type: single nucleotide variant
Location: chr11:77181443 (GRCh38)
Gene constraint: LOEUF 0.995 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 77.73 · 1 PDB
Residue 920: the 'sah' region

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

Similar variants

MYO7A p.Arg920Trp Uncertain significance ★★ ⚠ same residue
MYO7A p.Arg920Gln Uncertain significance ★ ⚠ same residue
MYO7A p.Arg920Gly Uncertain significance ★ ⚠ same residue
MYO7A p.Arg920Leu Conflicting classifications of pathogenicity ★ ⚠ 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

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-arg920 (accessed [today's date]).

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