Is MAPK8IP3 p.Val13= (c.39G>A) pathogenic?

MAPK8IP3 p.Val13= (c.39G>A) is classified Benign in MAPK8IP3 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-12-02). Common (popmax 7.91%, sas) — too common for a highly-penetrant pathogenic allele; Associated with MAPK8IP3-related disorder.

What condition is associated with MAPK8IP3 p.Val13= (c.39G>A)?

MAPK8IP3 p.Val13= (c.39G>A) is associated with MAPK8IP3-related disorder (ClinVar).

MAPK8IP3 p.Val13=

Q: How common is MAPK8IP3 p.Val13= (c.39G>A) in the general population?

MAPK8IP3 p.Val13= (c.39G>A) is common (popmax 7.91%, sas) — too common for a highly-penetrant pathogenic allele (gnomAD).

c.39G>A · rs201073807 · VCV3039422

Benign No assertion criteria

Classification

Benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Common

common (popmax 7.91%, sas) — too common for a highly-penetrant pathogenic allele

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 2	GERP -2.8, phastCons 1
Overall
CADD	11.79	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 7.91% South Asian · 7,156/90,480 alleles

Filtering AF 7.76% ClinGen BA1/BS1 input FAF95, joint · FAF99 7.69%

Overall 0.676% 10,883/1,610,328 alleles · common exomes 10,226/1,458,016 · genomes 657/152,312 · joint denominator

Ancestry group	Frequency	1 in
South Asiangrpmax	7.91%	13
Remaining individualsnot grpmax-eligible	0.708%	141
Ashkenazi Jewishnot grpmax-eligible	0.41%	244
European (non-Finnish)	0.249%	402
Middle Eastern	0.248%	403
Admixed American	0.211%	474
African / African-American	0.0761%	1,315
East Asian	0.0627%	1,595
Finnishnot grpmax-eligible	0.0127%	7,865

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.Val13=
Coding: c.39G>A
MANE Select: NM_001318852
dbSNP: rs201073807
Type: single nucleotide variant
Location: chr16:1706378 (GRCh38)
Gene constraint: LOEUF 0.407 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 63.19 · 5 PDB
Residue 13: the rh1 domain

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-val13 (accessed [today's date]).

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