Is PDCD10 p.Lys111fs (c.333del) pathogenic?

PDCD10 p.Lys111fs (c.333del) is classified Pathogenic in PDCD10 (ClinVar, Single submitter, 1 submitter; last evaluated 2019-10-31). No gnomAD frequency available for this variant; Associated with cerebral cavernous malformation 3.

What condition is associated with PDCD10 p.Lys111fs (c.333del)?

PDCD10 p.Lys111fs (c.333del) is associated with cerebral cavernous malformation 3 (ClinVar).

How common is PDCD10 p.Lys111fs (c.333del) in the general population?

PDCD10 p.Lys111fs (c.333del) is no gnomAD frequency available for this variant (gnomAD).

PDCD10 p.Lys111fs

c.333del · rs1559952317 · VCV1065419

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

cerebral cavernous malformation 3

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 12	GERP 2.1, phastCons 1

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

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. 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: PDCD10
Protein: p.Lys111fs
Coding: c.333del
MANE Select: NM_007217
dbSNP: rs1559952317
Type: Deletion
Location: chr3:167695658 (GRCh38)
Gene constraint: LOEUF 0.924 · pLI 0.64 (gnomAD)
Structure: AlphaFold pLDDT 90.82 · 10 PDB
Residue 111: an α-helix

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

Disease context

cerebral cavernous malformation 3 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

PDCD10 p.Gln112fs Pathogenic ★★ same condition
PDCD10 c.-117+6518_20del Pathogenic ★ same condition
PDCD10 p.Arg82fs Pathogenic ★ same condition
PDCD10 p.Asn55fs Pathogenic ★ same condition
PDCD10 p.Glu166fs Pathogenic ★ same condition
PDCD10 p.Glu52fs Pathogenic ★ same condition
PDCD10 p.Glu54fs Pathogenic ★ same condition
PDCD10 p.Ile131fs 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-lys111fs (accessed [today's date]).

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