Is MARK2 p.Gln88= (c.264A>G) pathogenic?

MARK2 p.Gln88= (c.264A>G) is classified Likely benign in MARK2 (ClinVar, Single submitter, 1 submitter; last evaluated 2018-07-23). Very rare (popmax 0.00446%, eas).

How common is MARK2 p.Gln88= (c.264A>G) in the general population?

MARK2 p.Gln88= (c.264A>G) is very rare (popmax 0.00446%, eas) (gnomAD).

MARK2 p.Gln88=

c.264A>G · rs760324570 · VCV764900

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00446%, eas)

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 -4.2	GERP -3.8
Overall
CADD	0.865	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00446% East Asian · 2/44,804 alleles

Filtering AF 0.00074% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000277%

Overall 0.000869% 14/1,611,272 alleles · very rare exomes 13/1,461,772 · genomes 1/149,500 · joint denominator

Ancestry group	Frequency	1 in
East Asiangrpmax	0.00446%	22,402
Remaining individualsnot grpmax-eligible	0.0032%	31,212
African / African-American	0.00271%	36,864
European (non-Finnish)	0.000678%	147,463

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: MARK2
Protein: p.Gln88=
Coding: c.264A>G
MANE Select: NM_001039469
dbSNP: rs760324570
Type: single nucleotide variant
Location: chr11:63895609 (GRCh38)
Gene constraint: LOEUF 0.287 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 68.21 · 5 PDB
Residue 88: the protein kinase domain; a UniProt-annotated variant site (in mrd76; likely pathogenic); an α-helix

Full MARK2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

MARK2 p.Gln88fs Uncertain significance ★ same residue
MARK2 p.Ala432Thr Uncertain significance ★★ ⚠ same type
MARK2 p.Arg264Ser Uncertain significance ★★ ⚠ same type
MARK2 p.Arg482Ter Uncertain significance ★★ same type
MARK2 c.337+8C>G Likely benign ★★ same type
MARK2 p.Pro459= Benign ★★ same type
MARK2 p.Pro740= Benign ★★ same type
MARK2 p.Ser725= Benign ★★ 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/mark2-p-gln88 (accessed [today's date]).

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