Is PDCD10 p.Ser71fs (c.211dup) pathogenic?

PDCD10 p.Ser71fs (c.211dup) is classified Pathogenic in PDCD10 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2022-11-24). Absent from gnomAD v4.1; Associated with cerebral cavernous malformation 3.

What condition is associated with PDCD10 p.Ser71fs (c.211dup)?

PDCD10 p.Ser71fs (c.211dup) is associated with cerebral cavernous malformation 3 (ClinVar).

How common is PDCD10 p.Ser71fs (c.211dup) in the general population?

PDCD10 p.Ser71fs (c.211dup) is absent from gnomAD v4.1 (gnomAD).

PDCD10 p.Ser71fs

c.211dup · rs2108409355 · VCV1076520

Pathogenic Multiple submitters

Classification

Pathogenic

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,611,932)

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 5 of 9
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 4.1	GERP 2.5, phastCons 1

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

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,611,932). 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.Ser71fs
Coding: c.211dup
MANE Select: NM_007217
dbSNP: rs2108409355
Type: Duplication
Location: chr3:167697065 (GRCh38)
Gene constraint: LOEUF 0.924 · pLI 0.64 (gnomAD)
Structure: AlphaFold pLDDT 90.82 · 10 PDB

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.Ser71Asn Uncertain significance ★ ⚠ same residue
PDCD10 p.Ser71= Likely benign ★ same residue
PDCD10 p.Asn195fs Pathogenic/Likely pathogenic ★★ same condition
PDCD10 p.Thr177fs Pathogenic/Likely pathogenic ★★ same condition
PDCD10 p.Ile198fs Pathogenic ★ same condition
PDCD10 p.Met26fs Likely pathogenic ★ same condition
PDCD10 p.Thr144fs Pathogenic ★ same condition
PDCD10 p.Thr77fs 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-ser71fs (accessed [today's date]).

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