Is MPL p.Asp47fs (c.139del) pathogenic?

MPL p.Asp47fs (c.139del) is classified Likely pathogenic in MPL (ClinVar, Single submitter, 1 submitter; last evaluated 2024-05-21). Very rare (popmax 0.00167%, amr); Associated with congenital amegakaryocytic thrombocytopenia.

What condition is associated with MPL p.Asp47fs (c.139del)?

MPL p.Asp47fs (c.139del) is associated with congenital amegakaryocytic thrombocytopenia (ClinVar).

How common is MPL p.Asp47fs (c.139del) in the general population?

MPL p.Asp47fs (c.139del) is very rare (popmax 0.00167%, amr) (gnomAD).

MPL p.Asp47fs

c.139del · VCV4815417

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Rare

very rare (popmax 0.00167%, amr)

Conditions

congenital amegakaryocytic thrombocytopenia

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function
NMD	predicted	premature termination codon in exon 2 of 12
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 11	GERP 2.1, phastCons 1

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00167% Admixed American · 1/60,024 alleles

Overall 6.2e-05% 1/1,614,178 alleles · very rare exomes 1/1,461,890 · genomes 0/152,288 · joint denominator

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: MPL
Protein: p.Asp47fs
Coding: c.139del
MANE Select: NM_005373
Type: Deletion
Location: chr1:43338157 (GRCh38)
Gene constraint: LOEUF 1.022 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 73.44 · 1 PDB

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

Disease context

congenital amegakaryocytic thrombocytopenia — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

MPL c.1653+1del Pathogenic/Likely pathogenic ★★ same condition
MPL p.Arg325fs Pathogenic/Likely pathogenic ★★ same condition
MPL p.Cys422fs Pathogenic/Likely pathogenic ★★ same condition
MPL p.Cys77fs Pathogenic/Likely pathogenic ★★ same condition
MPL p.Glu439fs Pathogenic/Likely pathogenic ★★ same condition
MPL p.Ile138fs Pathogenic/Likely pathogenic ★★ same condition
MPL p.Ile152fs Pathogenic/Likely pathogenic ★★ same condition
MPL p.Leu103fs Pathogenic/Likely pathogenic ★★ 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/mpl-p-asp47fs (accessed [today's date]).

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