Is PDCD10 p.Phe167fs (c.501del) pathogenic?

PDCD10 p.Phe167fs (c.501del) is classified Likely pathogenic in PDCD10 (ClinVar, Single submitter, 1 submitter; last evaluated 2013-10-04). Absent from gnomAD.

How common is PDCD10 p.Phe167fs (c.501del) in the general population?

PDCD10 p.Phe167fs (c.501del) is absent from gnomAD (gnomAD).

PDCD10 p.Phe167fs

c.501del · rs1559944592 · VCV590681

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

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 8 of 9
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 7.7	GERP 2.5, 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.Phe167fs
Coding: c.501del
MANE Select: NM_007217
dbSNP: rs1559944592
Type: Deletion
Location: chr3:167687290 (GRCh38)
Gene constraint: LOEUF 0.924 · pLI 0.64 (gnomAD)
Structure: AlphaFold pLDDT 90.82 · 10 PDB
Residue 167: an α-helix

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

Similar variants

PDCD10 p.Gln112fs Pathogenic ★★ same type
PDCD10 c.268+1del Likely pathogenic ★ same type
PDCD10 c.-117+6518_20del Pathogenic ★ same type
PDCD10 p.Ala40fs Likely pathogenic ★ same type
PDCD10 p.Arg82fs Pathogenic ★ same type
PDCD10 p.Asn189fs Likely pathogenic ★ same type
PDCD10 p.Asn55fs Pathogenic ★ same type
PDCD10 p.Glu166fs Pathogenic ★ same type

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-phe167fs (accessed [today's date]).

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