Is MYO7A p.Glu1716del (c.5143GAG[1]) pathogenic?

MYO7A p.Glu1716del (c.5143GAG[1]) is classified Pathogenic/Likely pathogenic in MYO7A (ClinVar, Multiple submitters, 4 submitters; last evaluated 2025-10-07). Very rare (popmax 0.00238%, sas); Associated with Usher syndrome.

What condition is associated with MYO7A p.Glu1716del (c.5143GAG[1])?

MYO7A p.Glu1716del (c.5143GAG[1]) is associated with Usher syndrome, Usher syndrome type 1, autosomal recessive nonsyndromic hearing loss 2 (ClinVar).

How common is MYO7A p.Glu1716del (c.5143GAG[1]) in the general population?

MYO7A p.Glu1716del (c.5143GAG[1]) is very rare (popmax 0.00238%, sas) (gnomAD).

How is Usher syndrome inherited?

Typically Autosomal recessive (Orphanet). A genetic counselor can assess individual risk for a family.

MYO7A p.Glu1716del

c.5143GAG[1] · rs1555102843 · VCV11864

Pathogenic/Likely pathogenic Multiple submitters

Classification

Pathogenic/Likely pathogenic

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 4 submitters

gnomAD v4.1

Rare

very rare (popmax 0.00238%, sas)

Conditions

Usher syndrome

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 7.9	GERP 1.8, phastCons 1

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00238% South Asian · 2/84,174 alleles

Filtering AF 0.000394% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000148%

Overall 0.000257% 4/1,554,004 alleles · very rare exomes 4/1,401,718 · genomes 0/152,286 · joint denominator

Ancestry group	Frequency	1 in
South Asiangrpmax	0.00238%	42,087
European (non-Finnish)	0.000174%	574,204

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.Glu1716del
Coding: c.5143GAG[1]
MANE Select: NM_000260
dbSNP: rs1555102843
Type: Microsatellite
Location: chr11:77202398 (GRCh38)
Gene constraint: LOEUF 0.995 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 77.73 · 1 PDB
Residue 1716: an α-helix

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

Disease context

Usher syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: Usher syndrome type 1 autosomal recessive nonsyndromic hearing loss 2 autosomal dominant nonsyndromic hearing loss 11 Usher syndrome type 1B

For Usher syndrome (Orphanet):

Inheritance: Autosomal recessive
Onset: Childhood, Infancy, Neonatal
Prevalence: 1-9 / 100 000 (Worldwide)

Similar variants

MYO7A p.Glu1716Ter Pathogenic/Likely pathogenic ★★ same residue
MYO7A p.Glu1716Lys Uncertain significance ★ ⚠ same residue
MYO7A p.Glu1716= Uncertain significance same residue
MYO7A p.Cys1198fs Pathogenic/Likely pathogenic ★★ same condition
MYO7A p.Leu1293fs Pathogenic/Likely pathogenic ★★ same condition
MYO7A p.Lys923del Likely pathogenic ★★ same condition
MYO7A p.Phe1963del Pathogenic/Likely pathogenic ★★ same condition
MYO7A p.Ser423fs Likely 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-glu1716del (accessed [today's date]).

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