Is MYO7A p.Arg900Cys (c.2698C>T) pathogenic?

MYO7A p.Arg900Cys (c.2698C>T) is classified Uncertain significance in MYO7A (ClinVar, Multiple submitters, 2 submitters; last evaluated 2025-06-15). AlphaMissense: ambiguous (0.503); Ultra-rare (popmax 0.0182%, mid).

How common is MYO7A p.Arg900Cys (c.2698C>T) in the general population?

MYO7A p.Arg900Cys (c.2698C>T) is ultra-rare (popmax 0.0182%, mid) (gnomAD).

What do computational predictors say about MYO7A p.Arg900Cys (c.2698C>T)?

AlphaMissense predicts ambiguous (score 0.503) — an in-silico prediction, not a clinical call.

MYO7A p.Arg900Cys

c.2698C>T · rs372849154 · VCV1408328

Uncertain significance Multiple submitters

Classification

Uncertain significance

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

AlphaMissense

ambiguous

0.503 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0182%, mid)

Missense predictors

2/2 damaging

REVEL, SaProt · AlphaMissense indeterminate

Computational evidence

Protein change
AlphaMissense	0.503	ambiguous
REVEL	0.85	moderately pathogenic-leaning
SaProt	LLR -11.30	damaging
⇒ REVEL and SaProt both call this damaging; AlphaMissense is indeterminate.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.6	GERP 1.6, phastCons 1
Regional constraint	o/e 0.95	unconstrained · MANE · 84 kb · p 0.0065 · regional, not allelic
Overall
CADD	32.0	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 0.0182% Middle Eastern · 1/5,506 alleles

Filtering AF 0.00394% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00361%

Overall 0.00423% 66/1,559,628 alleles · ultra-rare exomes 61/1,407,406 · genomes 5/152,222 · joint denominator

Ancestry group	Frequency	1 in
Middle Easterngrpmax	0.0182%	5,506
Admixed American	0.00767%	13,033
European (non-Finnish)	0.00503%	19,888
African / African-American	0.00408%	24,509

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.Arg900Cys
Coding: c.2698C>T
MANE Select: NM_000260
dbSNP: rs372849154
Type: single nucleotide variant
Location: chr11:77181383 (GRCh38)
Gene constraint: LOEUF 0.995 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 77.73 · 1 PDB
Residue 900: the 'sah' region

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

Similar variants

MYO7A p.Arg900His Uncertain significance ★★ ⚠ same residue
MYO7A p.Arg900Leu Uncertain significance ★ ⚠ same residue
MYO7A p.Ala1288Pro Likely pathogenic ★★★ same type
MYO7A p.Arg1168Gln Pathogenic ★★★ ⚠ same type
MYO7A p.Arg1873Gln Pathogenic ★★★ ⚠ same type
MYO7A p.Arg395Cys Likely pathogenic ★★★ ⚠ same type
MYO7A p.Arg668Cys Pathogenic ★★★ same type
MYO7A p.Arg853His Likely pathogenic ★★★ same type

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-arg900cys (accessed [today's date]).

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