Is MAPKBP1 p.Arg90= (c.270G>A) pathogenic?

MAPKBP1 p.Arg90= (c.270G>A) is classified Likely benign in MAPKBP1 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-11-13). Ultra-rare (popmax 0.0274%, sas); Associated with Inborn genetic diseases.

What condition is associated with MAPKBP1 p.Arg90= (c.270G>A)?

MAPKBP1 p.Arg90= (c.270G>A) is associated with Inborn genetic diseases (ClinVar).

How common is MAPKBP1 p.Arg90= (c.270G>A) in the general population?

MAPKBP1 p.Arg90= (c.270G>A) is ultra-rare (popmax 0.0274%, sas) (gnomAD).

MAPKBP1 p.Arg90=

c.270G>A · VCV4624303

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0274%, sas)

Conditions

Inborn genetic diseases

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.095	moderately benign-leaning
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 4.6	GERP -3.4, phastCons 1
Overall
CADD	16.38	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0274% South Asian · 25/91,092 alleles

Filtering AF 0.019% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0163%

Overall 0.00167% 27/1,614,230 alleles · ultra-rare exomes 26/1,461,890 · genomes 1/152,340 · joint denominator

Ancestry group	Frequency	1 in
South Asiangrpmax	0.0274%	3,644
Middle Eastern	0.0165%	6,062
European (non-Finnish)	8.47e-05%	1,180,044

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: MAPKBP1
Protein: p.Arg90=
Coding: c.270G>A
MANE Select: NM_014994
Type: single nucleotide variant
Location: chr15:41811178 (GRCh38)
Gene constraint: LOEUF 0.484 · pLI 0.84 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 62.82

Full MAPKBP1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

MAPKBP1 p.Ala1126Pro Uncertain significance ★★ ⚠ same condition
MAPKBP1 p.Ala1407Thr Uncertain significance ★★ ⚠ same condition
MAPKBP1 p.Ala1427Ser Uncertain significance ★★ ⚠ same condition
MAPKBP1 p.Ala146Thr Uncertain significance ★★ ⚠ same condition
MAPKBP1 p.Arg1314Trp Uncertain significance ★★ ⚠ same condition
MAPKBP1 p.Arg1337Ser Uncertain significance ★★ ⚠ same condition
MAPKBP1 p.Arg1425Cys Uncertain significance ★★ ⚠ same condition
MAPKBP1 p.Arg1506His 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/mapkbp1-p-arg90 (accessed [today's date]).

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