Is MAPK8IP3 p.Asp1302= (c.3906C>T) pathogenic?

MAPK8IP3 p.Asp1302= (c.3906C>T) is classified Likely benign in MAPK8IP3 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2020-10-06). Ultra-rare (popmax 0.0227%, afr); Associated with MAPK8IP3-related disorder.

What condition is associated with MAPK8IP3 p.Asp1302= (c.3906C>T)?

MAPK8IP3 p.Asp1302= (c.3906C>T) is associated with MAPK8IP3-related disorder (ClinVar).

How common is MAPK8IP3 p.Asp1302= (c.3906C>T) in the general population?

MAPK8IP3 p.Asp1302= (c.3906C>T) is ultra-rare (popmax 0.0227%, afr) (gnomAD).

MAPK8IP3 p.Asp1302=

c.3906C>T · rs368321815 · VCV3048126

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0227%, afr)

Conditions

MAPK8IP3-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 -11	GERP -3.5
Overall
CADD	0.128	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0227% African / African-American · 17/74,838 alleles

Filtering AF 0.0144% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0119%

Overall 0.00155% 25/1,611,574 alleles · ultra-rare exomes 9/1,459,524 · genomes 16/152,050 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.0227%	4,402
East Asian	0.00669%	14,954
Remaining individualsnot grpmax-eligible	0.0032%	31,211
Admixed American	0.00167%	59,978
European (non-Finnish)	0.00017%	589,525

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: MAPK8IP3
Protein: p.Asp1302=
Coding: c.3906C>T
MANE Select: NM_001318852
dbSNP: rs368321815
Type: single nucleotide variant
Location: chr16:1768716 (GRCh38)
Gene constraint: LOEUF 0.407 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 63.19 · 5 PDB
Residue 1302: the 'disordered' region; a UniProt-annotated variant site (in nedba)

Full MAPK8IP3 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

MAPK8IP3-related disorder

Similar variants

MAPK8IP3 p.Tyr37Ter Likely pathogenic ★★ same condition
MAPK8IP3 c.1098-4A>G Uncertain significance ★ same condition
MAPK8IP3 p.Asn1189Lys Uncertain significance ★ ⚠ same condition
MAPK8IP3 p.Asn1282Lys Uncertain significance ★ ⚠ same condition
MAPK8IP3 p.Asp1058Asn Uncertain significance ★ ⚠ same condition
MAPK8IP3 p.Met25Ile Uncertain significance ★ ⚠ same condition
MAPK8IP3 p.Ser820Asn Uncertain significance ★ ⚠ same condition
MAPK8IP3 p.Ala1150Val 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/mapk8ip3-p-asp1302 (accessed [today's date]).

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