Is MAPKBP1 p.Pro1124= (c.3372A>T) pathogenic?

MAPKBP1 p.Pro1124= (c.3372A>T) is classified Likely benign in MAPKBP1 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2024-02-01). Absent from gnomAD v4.1; Associated with MAPKBP1-related disorder.

What condition is associated with MAPKBP1 p.Pro1124= (c.3372A>T)?

MAPKBP1 p.Pro1124= (c.3372A>T) is associated with MAPKBP1-related disorder (ClinVar).

How common is MAPKBP1 p.Pro1124= (c.3372A>T) in the general population?

MAPKBP1 p.Pro1124= (c.3372A>T) is absent from gnomAD v4.1 (gnomAD).

MAPKBP1 p.Pro1124=

c.3372A>T · rs2551106871 · VCV3032346

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

MAPKBP1-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 -0.07	GERP -3.1
Overall
CADD	6.133	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: MAPKBP1
Protein: p.Pro1124=
Coding: c.3372A>T
MANE Select: NM_014994
dbSNP: rs2551106871
Type: single nucleotide variant
Location: chr15:41822996 (GRCh38)
Gene constraint: LOEUF 0.484 · pLI 0.84 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 62.82
Residue 1124: the 'disordered' region

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

Disease context

MAPKBP1-related disorder

Similar variants

MAPKBP1 p.Gln1449Ter Likely pathogenic ★ same condition
MAPKBP1 c.2156+1G>A Likely pathogenic same condition
MAPKBP1 p.Arg850Cys Uncertain significance same condition
MAPKBP1 p.Asn956Ser Uncertain significance ⚠ same condition
MAPKBP1 p.Gln1366Glu Uncertain significance ⚠ same condition
MAPKBP1 c.114+10G>T Likely benign same condition
MAPKBP1 c.1782+9G>A Likely benign same condition
MAPKBP1 p.Asp1293= Likely benign 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-pro1124 (accessed [today's date]).

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