Is MAPKAPK3 p.Arg282= (c.846C>T) pathogenic?

MAPKAPK3 p.Arg282= (c.846C>T) is classified Likely benign in MAPKAPK3 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-02-24). Absent from gnomAD v4.1.

How common is MAPKAPK3 p.Arg282= (c.846C>T) in the general population?

MAPKAPK3 p.Arg282= (c.846C>T) is absent from gnomAD v4.1 (gnomAD).

MAPKAPK3 p.Arg282=

c.846C>T · rs781279860 · VCV1079396

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.016	strongly benign-leaning
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP 0.03	GERP -3.1, phastCons 0.043
Overall
CADD	7.258	PHRED · no single calibrated threshold — expert panels disagree

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: MAPKAPK3
Protein: p.Arg282=
Coding: c.846C>T
MANE Select: NM_001243925
dbSNP: rs781279860
Type: single nucleotide variant
Location: chr3:50646756 (GRCh38)
Gene constraint: LOEUF 0.943 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 83.10 · 5 PDB
Residue 282: the protein kinase domain; an α-helix

Full MAPKAPK3 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

MAPKAPK3 p.Arg282Cys Uncertain significance ★★ ⚠ same residue
MAPKAPK3 p.Arg282His Uncertain significance ★★ ⚠ same residue
MAPKAPK3 p.Ala181Ser Uncertain significance ★★ ⚠ same type
MAPKAPK3 p.Arg112His Uncertain significance ★★ ⚠ same type
MAPKAPK3 p.Arg148Gln Uncertain significance ★★ ⚠ same type
MAPKAPK3 p.Arg148Trp Uncertain significance ★★ ⚠ same type
MAPKAPK3 p.Arg259Cys Uncertain significance ★★ same type
MAPKAPK3 p.Arg319Gln Uncertain significance ★★ ⚠ 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/mapkapk3-p-arg282 (accessed [today's date]).

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