Is MAPKBP1 p.Ala68= (c.204A>T) pathogenic?

MAPKBP1 p.Ala68= (c.204A>T) is classified Likely benign in MAPKBP1 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-03-01). No allele count reported in gnomAD v4.1 (AN 1,613,742).

How common is MAPKBP1 p.Ala68= (c.204A>T) in the general population?

MAPKBP1 p.Ala68= (c.204A>T) is no allele count reported in gnomAD v4.1 (AN 1,613,742) (gnomAD).

MAPKBP1 p.Ala68=

c.204A>T · VCV3778067

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,613,742)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.01	strongly benign-leaning
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.19	GERP -3.1, phastCons 0.99
Overall
CADD	10.32	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,613,742). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: MAPKBP1
Protein: p.Ala68=
Coding: c.204A>T
MANE Select: NM_014994
Type: single nucleotide variant
Location: chr15:41799912 (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

Similar variants

MAPKBP1 c.1711+5G>A Uncertain significance ★★ same type
MAPKBP1 p.Ala1126Pro Uncertain significance ★★ ⚠ same type
MAPKBP1 p.Ala1407Thr Uncertain significance ★★ ⚠ same type
MAPKBP1 p.Ala1427Ser Uncertain significance ★★ ⚠ same type
MAPKBP1 p.Ala146Thr Uncertain significance ★★ ⚠ same type
MAPKBP1 p.Arg1102Cys Uncertain significance ★★ ⚠ same type
MAPKBP1 p.Arg1314Trp Uncertain significance ★★ ⚠ same type
MAPKBP1 p.Arg1337Ser 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/mapkbp1-p-ala68 (accessed [today's date]).

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