Is MYO7A p.Arg1967Ter (c.5899C>T) pathogenic?

MYO7A p.Arg1967Ter (c.5899C>T) is classified Pathogenic/Likely pathogenic in MYO7A (ClinVar, Multiple submitters, 11 submitters; last evaluated 2024-09-22). Very rare (popmax 0.0022%, sas); Associated with autosomal recessive nonsyndromic hearing loss 2.

What condition is associated with MYO7A p.Arg1967Ter (c.5899C>T)?

MYO7A p.Arg1967Ter (c.5899C>T) is associated with autosomal recessive nonsyndromic hearing loss 2, Usher syndrome type 1, autosomal dominant nonsyndromic hearing loss 11 (ClinVar).

How common is MYO7A p.Arg1967Ter (c.5899C>T) in the general population?

MYO7A p.Arg1967Ter (c.5899C>T) is very rare (popmax 0.0022%, sas) (gnomAD).

MYO7A p.Arg1967Ter

c.5899C>T · rs376764423 · VCV178495

Pathogenic/Likely pathogenic Multiple submitters

Classification

Pathogenic/Likely pathogenic

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 11 submitters

Consequence

nonsense (stop-gain)

predicted LoF

gnomAD v4.1

Rare

very rare (popmax 0.0022%, sas)

Conditions

autosomal recessive nonsyndromic hearing loss 2

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal.
Consequence	nonsense (stop-gain)	predicted loss-of-function
NMD	predicted	premature termination codon in exon 43 of 49
Splicing
SpliceAI	Δ0.46	acceptor loss, 42 bp away · masked 0 · deltas
Pangolin	Δ0.62	loss · gain 0.20 · agrees with SpliceAI · independent
Constraint at this position
Conservation	phyloP 4.9	GERP 1.6, phastCons 1
Overall
CADD	57.0	PHRED · no single calibrated threshold — expert panels disagree

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

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0022% South Asian · 2/90,978 alleles

Filtering AF 0.000365% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000159%

Overall 0.000558% 9/1,613,572 alleles · very rare exomes 6/1,461,392 · genomes 3/152,180 · joint denominator

Ancestry group	Frequency	1 in
South Asiangrpmax	0.0022%	45,489
European (non-Finnish)	0.000593%	168,539

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.Arg1967Ter
Coding: c.5899C>T
MANE Select: NM_000260
dbSNP: rs376764423
Type: single nucleotide variant
Location: chr11:77208472 (GRCh38)
Gene constraint: LOEUF 0.995 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 77.73 · 1 PDB
Residue 1967: the ferm 2 domain; an α-helix

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

Disease context

autosomal recessive nonsyndromic hearing loss 2 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: Usher syndrome type 1 autosomal dominant nonsyndromic hearing loss 11 inherited retinal dystrophy Usher syndrome type 1B

Similar variants

MYO7A p.Arg1967Gly Uncertain significance ★ ⚠ same residue
MYO7A p.Arg1967Gln Uncertain significance ★★ ⚠ 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

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-arg1967ter (accessed [today's date]).

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