Is MYO7A p.Leu2068Arg (c.6203T>G) pathogenic?

MYO7A p.Leu2068Arg (c.6203T>G) is classified Uncertain significance in MYO7A (ClinVar, Multiple submitters, 5 submitters; last evaluated 2025-07-03). AlphaMissense: likely benign (0.3137); Ultra-rare (popmax 0.0371%, sas); Associated with Inborn genetic diseases.

What condition is associated with MYO7A p.Leu2068Arg (c.6203T>G)?

MYO7A p.Leu2068Arg (c.6203T>G) is associated with Inborn genetic diseases, Usher syndrome type 1, autosomal recessive nonsyndromic hearing loss 2 (ClinVar).

How common is MYO7A p.Leu2068Arg (c.6203T>G) in the general population?

MYO7A p.Leu2068Arg (c.6203T>G) is ultra-rare (popmax 0.0371%, sas) (gnomAD).

What do computational predictors say about MYO7A p.Leu2068Arg (c.6203T>G)?

AlphaMissense predicts likely benign (score 0.3137) — an in-silico prediction, not a clinical call.

MYO7A p.Leu2068Arg

c.6203T>G · rs779090765 · VCV374617

Uncertain significance Multiple submitters

Classification

Uncertain significance

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 5 submitters

AlphaMissense

likely benign

0.3137 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0371%, sas)

Missense predictors

1/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.3137	likely benign
REVEL	0.779	moderately pathogenic-leaning
SaProt	LLR -8.44	tolerated
⇒ REVEL calls this damaging; AlphaMissense and SaProt do not.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.9	GERP 1.8, phastCons 1
Regional constraint	o/e 0.95	unconstrained · MANE · 84 kb · p 0.0065 · regional, not allelic
Overall
CADD	24.4	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0371% South Asian · 32/86,178 alleles

Filtering AF 0.027% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0235%

Overall 0.00354% 56/1,583,152 alleles · ultra-rare exomes 53/1,430,980 · genomes 3/152,172 · joint denominator

Ancestry group	Frequency	1 in
South Asiangrpmax	0.0371%	2,693
Remaining individualsnot grpmax-eligible	0.00815%	12,276
Admixed American	0.00181%	55,386
European (non-Finnish)	0.00154%	64,727

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.Leu2068Arg
Coding: c.6203T>G
MANE Select: NM_000260
dbSNP: rs779090765
Type: single nucleotide variant
Location: chr11:77211303 (GRCh38)
Gene constraint: LOEUF 0.995 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 77.73 · 1 PDB
Residue 2068: the ferm 2 domain; a turn

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

Disease context

Inborn genetic diseases — 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

Similar variants

MYO7A p.Leu2068= Likely benign ★ same residue
MYO7A p.Ala1288Pro Likely pathogenic ★★★ same condition
MYO7A p.Arg1168Gln Pathogenic ★★★ ⚠ same condition
MYO7A p.Arg1873Gln Pathogenic ★★★ ⚠ same condition
MYO7A p.Arg395Cys Likely pathogenic ★★★ ⚠ same condition
MYO7A p.Arg668Cys Pathogenic ★★★ same condition
MYO7A p.Arg853His Likely pathogenic ★★★ same condition
MYO7A p.Glu968Asp 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-leu2068arg (accessed [today's date]).

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