Is MYO7B p.Ser678= (c.2034G>A) pathogenic?

MYO7B p.Ser678= (c.2034G>A) is classified Likely benign in MYO7B (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-04-01). Ultra-rare (popmax 0.0365%, sas); Associated with MYO7B-related disorder.

What condition is associated with MYO7B p.Ser678= (c.2034G>A)?

MYO7B p.Ser678= (c.2034G>A) is associated with MYO7B-related disorder (ClinVar).

How common is MYO7B p.Ser678= (c.2034G>A) in the general population?

MYO7B p.Ser678= (c.2034G>A) is ultra-rare (popmax 0.0365%, sas) (gnomAD).

MYO7B p.Ser678=

c.2034G>A · rs370974785 · VCV3052268

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0365%, sas)

Conditions

MYO7B-related disorder

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP -20	GERP -4.1
Overall
CADD	0.075	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0365% South Asian · 33/90,492 alleles

Filtering AF 0.0267% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0233%

Overall 0.0041% 66/1,610,180 alleles · ultra-rare exomes 63/1,457,944 · genomes 3/152,236 · joint denominator

Ancestry group	Frequency	1 in
South Asiangrpmax	0.0365%	2,742
Middle Eastern	0.0165%	6,076
Remaining individualsnot grpmax-eligible	0.00642%	15,564
East Asian	0.00447%	22,392
Admixed American	0.00334%	29,902
European (non-Finnish)	0.00204%	49,124

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.Ser678=
Coding: c.2034G>A
MANE Select: NM_001393586
dbSNP: rs370974785
Type: single nucleotide variant
Location: chr2:127592835 (GRCh38)
Gene constraint: LOEUF 0.956 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 78.34 · 3 PDB
Residue 678: the myosin motor domain

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-ser678 (accessed [today's date]).

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