Is PDCD10 p.Arg124fs (c.372_373del) pathogenic?

PDCD10 p.Arg124fs (c.372373del) is classified Pathogenic in PDCD10 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2024-09-02). Associated with PDCD10-related disorder.

What condition is associated with PDCD10 p.Arg124fs (c.372_373del)?

PDCD10 p.Arg124fs (c.372_373del) is associated with PDCD10-related disorder, cerebral cavernous malformation 3 (ClinVar).

PDCD10 p.Arg124fs

c.372_373del · VCV3720543

Pathogenic Multiple submitters

Classification

Pathogenic

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

Consequence

frameshift

predicted LoF

gnomAD v4.1

Rare

Conditions

PDCD10-related disorder

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 6 of 9
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 11	GERP 1.2, phastCons 1

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

Variant & gene context

Gene: PDCD10
Protein: p.Arg124fs
Coding: c.372_373del
MANE Select: NM_007217
Type: Microsatellite
Location: chr3:167695618 (GRCh38)
Gene constraint: LOEUF 0.924 · pLI 0.64 (gnomAD)
Structure: AlphaFold pLDDT 90.82 · 10 PDB
Residue 124: an α-helix

Full PDCD10 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

PDCD10-related disorder

Also linked: cerebral cavernous malformation 3

Similar variants

PDCD10 c.557+4_557+7del Pathogenic/Likely pathogenic ★★ same condition
PDCD10 p.Met92fs Pathogenic ★ same condition
PDCD10 p.Ile49del Uncertain significance ★ same condition
PDCD10 c.396-2A>G Pathogenic ★★ same condition
PDCD10 c.474+5G>A Pathogenic/Likely pathogenic ★★ same condition
PDCD10 c.557+1G>A Pathogenic ★★ same condition
PDCD10 p.Arg108Ter Pathogenic ★★ same condition
PDCD10 p.Arg196Ter 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/pdcd10-p-arg124fs (accessed [today's date]).

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