Is ADAMTS2 p.Pro46fs (c.137del) pathogenic?

ADAMTS2 p.Pro46fs (c.137del) is classified Pathogenic/Likely pathogenic in ADAMTS2 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2024-03-02). Very rare (popmax 0.000109%, nfe); Associated with Ehlers-Danlos syndrome, dermatosparaxis type.

What condition is associated with ADAMTS2 p.Pro46fs (c.137del)?

ADAMTS2 p.Pro46fs (c.137del) is associated with Ehlers-Danlos syndrome, dermatosparaxis type (ClinVar).

How common is ADAMTS2 p.Pro46fs (c.137del) in the general population?

ADAMTS2 p.Pro46fs (c.137del) is very rare (popmax 0.000109%, nfe) (gnomAD).

How is Dermatosparaxis Ehlers-Danlos syndrome inherited?

Typically Autosomal recessive (Orphanet). A genetic counselor can assess individual risk for a family.

ADAMTS2 p.Pro46fs

c.137del · rs1417947464 · VCV1072866

Pathogenic/Likely pathogenic Multiple submitters

Classification

Pathogenic/Likely pathogenic

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

Consequence

frameshift

predicted LoF

gnomAD v4.1

Rare

very rare (popmax 0.000109%, nfe)

Conditions

Ehlers-Danlos syndrome, dermatosparaxis type

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 1 of 22
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP -0.012	GERP -1.6, phastCons 0.86

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

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.000109% European (non-Finnish) · 1/914,710 alleles

Overall 0.000104% 1/958,932 alleles · very rare

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: ADAMTS2
Protein: p.Pro46fs
Coding: c.137del
MANE Select: NM_014244
dbSNP: rs1417947464
Type: Deletion
Location: chr5:179345192 (GRCh38)
Gene constraint: LOEUF 0.568 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 71.59

Full ADAMTS2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Ehlers-Danlos syndrome, dermatosparaxis type — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Dermatosparaxis Ehlers-Danlos syndrome (Orphanet):

Inheritance: Autosomal recessive
Onset: Infancy, Neonatal

Similar variants

ADAMTS2 p.Pro46Gln Uncertain significance ★★ ⚠ same residue
ADAMTS2 p.Pro46= Conflicting classifications of pathogenicity ★ same residue
ADAMTS2 c.689-9_695del Likely pathogenic ★★ same condition
ADAMTS2 p.Ala89fs Pathogenic/Likely pathogenic ★★ same condition
ADAMTS2 p.Met791fs Pathogenic/Likely pathogenic ★★ same condition
ADAMTS2 p.Pro33fs Pathogenic/Likely pathogenic ★★ same condition
ADAMTS2 p.Pro34fs Pathogenic/Likely pathogenic ★★ same condition
ADAMTS2 p.Tyr834_Met835insTer 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/adamts2-p-pro46fs (accessed [today's date]).

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