Is MARK2 p.Ala80Val (c.239C>T) pathogenic?

MARK2 p.Ala80Val (c.239C>T) is classified Pathogenic/Likely pathogenic in MARK2 (ClinVar, No assertion criteria, 2 submitters; last evaluated 2025-07-25). AlphaMissense: likely pathogenic (0.9987); Absent from gnomAD v4.1; Associated with autism spectrum disorder.

What condition is associated with MARK2 p.Ala80Val (c.239C>T)?

MARK2 p.Ala80Val (c.239C>T) is associated with autism spectrum disorder, intellectual developmental disorder, autosomal dominant 76 (ClinVar).

How common is MARK2 p.Ala80Val (c.239C>T) in the general population?

MARK2 p.Ala80Val (c.239C>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about MARK2 p.Ala80Val (c.239C>T)?

AlphaMissense predicts likely pathogenic (score 0.9987) — an in-silico prediction, not a clinical call.

MARK2 p.Ala80Val

c.239C>T · rs2539306253 · VCV3253643

Pathogenic/Likely pathogenic No assertion criteria

Classification

Pathogenic/Likely pathogenic

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 2 submitters

AlphaMissense

likely pathogenic

0.9987 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

2/2 damaging

AlphaMissense, SaProt · REVEL indeterminate

Conditions

autism spectrum disorder

Computational evidence

Protein change
AlphaMissense	0.9987	likely pathogenic ✓ concordant with ClinVar
REVEL	0.624	indeterminate
SaProt	LLR -14.98	damaging
⇒ AlphaMissense and SaProt both call this damaging; REVEL is indeterminate.
Splicing
SpliceAI	<0.2	all four deltas below 0.2 · C>A here scores Δ0.28 · evaluated, not missing
Constraint at this position
Conservation	phyloP 7.7	GERP 1.9, phastCons 1
Regional constraint	o/e 0.29	constrained · MANE · 5,393 bp · p 7.7e-34 · regional, not allelic
Overall
CADD	33.0	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

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: MARK2
Protein: p.Ala80Val
Coding: c.239C>T
MANE Select: NM_001039469
dbSNP: rs2539306253
Type: single nucleotide variant
Location: chr11:63895584 (GRCh38)
Gene constraint: LOEUF 0.287 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 68.21 · 5 PDB
Residue 80: the protein kinase domain; a UniProt-annotated variant site (in mrd76; likely pathogenic); a β-strand

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

Disease context

autism spectrum disorder — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: intellectual developmental disorder, autosomal dominant 76

Similar variants

MARK2 p.Ala432Thr Uncertain significance ★★ ⚠ same condition
MARK2 c.1934+1G>A Likely pathogenic ★ same condition
MARK2 c.2006+2T>G Likely pathogenic ★ same condition
MARK2 c.337+1G>T Pathogenic ★ same condition
MARK2 p.Arg584Ter Pathogenic ★ same condition
MARK2 p.Gly135Arg Likely pathogenic ★ same condition
MARK2 c.1101+5G>A Uncertain significance ★ same condition
MARK2 p.Arg302Ter Uncertain significance ★ 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/mark2-p-ala80val (accessed [today's date]).

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