Is MARK3 p.Gln50= (c.150A>G) pathogenic?

MARK3 p.Gln50= (c.150A>G) is classified Likely benign in MARK3 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-09-20). Ultra-rare (popmax 0.0832%, mid); Associated with MARK3-related disorder.

What condition is associated with MARK3 p.Gln50= (c.150A>G)?

MARK3 p.Gln50= (c.150A>G) is associated with MARK3-related disorder (ClinVar).

How common is MARK3 p.Gln50= (c.150A>G) in the general population?

MARK3 p.Gln50= (c.150A>G) is ultra-rare (popmax 0.0832%, mid) (gnomAD).

MARK3 p.Gln50=

c.150A>G · rs750895691 · VCV3040090

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0832%, mid)

Conditions

MARK3-related disorder

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -0.6	GERP -5.7
Overall
CADD	4.102	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0832% Middle Eastern · 5/6,010 alleles

Filtering AF 0.0327% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0213%

Overall 0.00163% 26/1,599,764 alleles · ultra-rare exomes 23/1,447,508 · genomes 3/152,256 · joint denominator

Ancestry group	Frequency	1 in
Middle Easterngrpmax	0.0832%	1,202
South Asian	0.00681%	14,688
European (non-Finnish)	0.00128%	78,418

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: MARK3
Protein: p.Gln50=
Coding: c.150A>G
MANE Select: NM_001128918
dbSNP: rs750895691
Type: single nucleotide variant
Location: chr14:103405174 (GRCh38)
Gene constraint: LOEUF 0.73 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 69.25 · 14 PDB

Full MARK3 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

MARK3-related disorder

Similar variants

MARK3 c.1586+4G>C Likely benign same condition
MARK3 c.412+4A>T Likely benign same condition
MARK3 p.Ala431= Benign same condition
MARK3 p.Asn632= Likely benign same condition
MARK3 p.Gly296Arg Likely benign same condition
MARK3 p.Leu625= Likely benign same condition
MARK3 p.Lys463= Benign same condition
MARK3 p.Ser443Gly 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/mark3-p-gln50 (accessed [today's date]).

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