Is MYO7A p.Arg1856fs (c.5567del) pathogenic?

MYO7A p.Arg1856fs (c.5567del) is classified Pathogenic in MYO7A (ClinVar, Single submitter, 1 submitter; last evaluated 2021-07-10). No gnomAD frequency available for this variant; Associated with ear malformation.

What condition is associated with MYO7A p.Arg1856fs (c.5567del)?

MYO7A p.Arg1856fs (c.5567del) is associated with ear malformation (ClinVar).

How common is MYO7A p.Arg1856fs (c.5567del) in the general population?

MYO7A p.Arg1856fs (c.5567del) is no gnomAD frequency available for this variant (gnomAD).

MYO7A p.Arg1856fs

c.5567del · rs2135733393 · VCV1180739

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

ear malformation

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function
NMD	predicted	premature termination codon in exon 40 of 49
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 4	GERP 1.2, phastCons 1

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. 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: MYO7A
Protein: p.Arg1856fs
Coding: c.5567del
MANE Select: NM_000260
dbSNP: rs2135733393
Type: Deletion
Location: chr11:77205548 (GRCh38)
Gene constraint: LOEUF 0.995 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 77.73 · 1 PDB
Residue 1856: the myth4 2 domain; an α-helix

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

Disease context

ear malformation — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

MYO7A p.Arg1856_Gln1859del Conflicting classifications of pathogenicity ★ same residue
MYO7A p.Arg1856Cys Uncertain significance ★★ ⚠ same residue
MYO7A p.Ala26fs Likely pathogenic ★ same condition
MYO7A p.Arg1856His Uncertain significance ★ ⚠ same residue
MYO7A c.1344-2A>G Pathogenic ★★ same condition
MYO7A p.Arg1240Trp Pathogenic/Likely pathogenic ★★ same condition
MYO7A p.Arg1739Ter Pathogenic ★★ same condition
MYO7A p.Arg570Ter 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/myo7a-p-arg1856fs (accessed [today's date]).

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