Is MYO7A p.Lys1210Ter (c.3628A>T) pathogenic?

MYO7A p.Lys1210Ter (c.3628A>T) is classified Pathogenic in MYO7A (ClinVar, Single submitter, 2 submitters; last evaluated 2023-06-09). Very rare (popmax 0.000424%, nfe); Associated with inherited retinal dystrophy.

What condition is associated with MYO7A p.Lys1210Ter (c.3628A>T)?

MYO7A p.Lys1210Ter (c.3628A>T) is associated with inherited retinal dystrophy (ClinVar).

How common is MYO7A p.Lys1210Ter (c.3628A>T) in the general population?

MYO7A p.Lys1210Ter (c.3628A>T) is very rare (popmax 0.000424%, nfe) (gnomAD).

MYO7A p.Lys1210Ter

c.3628A>T · rs878853376 · VCV236485

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 2 submitters

Consequence

nonsense (stop-gain)

predicted LoF

gnomAD v4.1

Rare

very rare (popmax 0.000424%, nfe)

Conditions

inherited retinal dystrophy

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	nonsense (stop-gain)	predicted loss-of-function
NMD	predicted	premature termination codon in exon 28 of 49
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 11	GERP 1.8, phastCons 1
Overall
CADD	48.0	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 0.000424% European (non-Finnish) · 5/1,179,798 alleles

Filtering AF 0.000124% ClinGen BA1/BS1 input FAF95, joint · FAF99 9e-05%

Overall 0.00031% 5/1,613,656 alleles · very rare exomes 5/1,461,518 · genomes 0/152,138 · joint denominator

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.Lys1210Ter
Coding: c.3628A>T
MANE Select: NM_000260
dbSNP: rs878853376
Type: single nucleotide variant
Location: chr11:77189468 (GRCh38)
Gene constraint: LOEUF 0.995 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 77.73 · 1 PDB
Residue 1210: the myth4 1 domain

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

Disease context

inherited retinal dystrophy — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

MYO7A p.Lys1210= Uncertain significance ★★ same residue
MYO7A p.Ala1288Pro Likely pathogenic ★★★ same condition
MYO7A p.Arg1168Gln Pathogenic ★★★ ⚠ same condition
MYO7A p.Glu968Asp Likely pathogenic ★★★ ⚠ same condition
MYO7A p.Val1372Gly Likely pathogenic ★★★ same condition
MYO7A p.Arg302His Likely benign ★★★ ⚠ same condition
MYO7A c.2283-1G>T Pathogenic ★★ same condition
MYO7A c.3109-2A>G Pathogenic/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-lys1210ter (accessed [today's date]).

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