Is MYO7B p.Arg2029Gln (c.6086G>A) pathogenic?

MYO7B p.Arg2029Gln (c.6086G>A) is classified Benign in MYO7B (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-02-20). AlphaMissense: likely benign (0.0859); Low-frequency (popmax 1.01%, sas); Associated with MYO7B-related disorder.

What condition is associated with MYO7B p.Arg2029Gln (c.6086G>A)?

MYO7B p.Arg2029Gln (c.6086G>A) is associated with MYO7B-related disorder (ClinVar).

How common is MYO7B p.Arg2029Gln (c.6086G>A) in the general population?

MYO7B p.Arg2029Gln (c.6086G>A) is low-frequency (popmax 1.01%, sas) (gnomAD).

What do computational predictors say about MYO7B p.Arg2029Gln (c.6086G>A)?

AlphaMissense predicts likely benign (score 0.0859) — an in-silico prediction, not a clinical call.

MYO7B p.Arg2029Gln

c.6086G>A · rs200072803 · VCV3049752

Benign No assertion criteria

Classification

Benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0859 · ACMG-weighted

gnomAD v4.1

Rare

low-frequency (popmax 1.01%, sas)

Missense predictors

0/2 damaging

AlphaMissense, SaProt · REVEL indeterminate

Conditions

MYO7B-related disorder

Computational evidence

Protein change
AlphaMissense	0.0859	likely benign
REVEL	0.51	indeterminate
SaProt	LLR -3.88	tolerated
⇒ AlphaMissense and SaProt both call this tolerated; REVEL is indeterminate.
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP 4	GERP -0.45, phastCons 1
Regional constraint	o/e 1.07	unconstrained · MANE · 7,741 bp · p 0.063 · regional, not allelic
Overall
CADD	24.5	PHRED · no single calibrated threshold — expert panels disagree

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

⚠ Isoform check: AlphaMissense numbered on a different transcript (AM R2003Q vs ClinVar R2029Q) — verify the residue.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 1.01% South Asian · 922/91,078 alleles

Filtering AF 0.958% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.936%

Overall 0.113% 1,822/1,613,562 alleles · low-frequency exomes 1,694/1,461,290 · genomes 128/152,272 · joint denominator

Ancestry group	Frequency	1 in
South Asiangrpmax	1.01%	99
Middle Eastern	0.38%	263
Remaining individualsnot grpmax-eligible	0.166%	601
Admixed American	0.0717%	1,395
European (non-Finnish)	0.0592%	1,690
East Asian	0.0267%	3,739
Finnishnot grpmax-eligible	0.0173%	5,793
African / African-American	0.0107%	9,378
Ashkenazi Jewishnot grpmax-eligible	0.00338%	29,600

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: MYO7B
Protein: p.Arg2029Gln
Coding: c.6086G>A
MANE Select: NM_001393586
dbSNP: rs200072803
Type: single nucleotide variant
Location: chr2:127636287 (GRCh38)
Gene constraint: LOEUF 0.956 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 78.34 · 3 PDB
Residue 2003 UniProt numbering: the ferm 2 domain; the 'mediates interaction with cdhr2, cdhr5 and ush1c' region

Full MYO7B gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

MYO7B-related disorder

Similar variants

MYO7B p.Ala397Ser Uncertain significance ⚠ same condition
MYO7B c.1081-10G>T Benign same condition
MYO7B c.1691-7T>C Benign same condition
MYO7B c.2339+4C>T Benign same condition
MYO7B c.4333+8C>A Likely benign same condition
MYO7B c.5714-7C>T Benign same condition
MYO7B c.5821-8T>C Benign same condition
MYO7B c.6123+9T>C Benign 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/myo7b-p-arg2029gln (accessed [today's date]).

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