PDCD2

Chr 6

programmed cell death 2

Also known as: RP8, ZMYND7

NCBI Gene: 5134 ENSG00000071994 UniProt: Q16342 OMIM: 600866

This protein functions as a chaperone for ribosomal protein uS5, cotranslationally associating with uS5 and accompanying it to ribosomal assembly sites in the nucleus. The gene is not highly constrained against loss-of-function variants and currently lacks established disease associations in OMIM, though it appears to function redundantly with PDCD2L in ribosomal protein chaperoning.

OMIM ResearchSummary from RefSeq, UniProt

This gene encodes a nuclear protein expressed in a variety of tissues. Expression of this gene has been shown to be repressed by B-cell CLL/lymphoma 6 (BCL6), a transcriptional repressor required for lymph node germinal center development, suggesting that BCL6 regulates apoptosis by its effects on this protein. Alternative splicing results in multiple transcript variants and pseudogenes have been identified on chromosomes 9 and 12. [provided by RefSeq, Dec 2010]

OMIM ResearchGenerating clinical summary…

LOEUF 1.37

Clinical Summary— PDCD2

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Population Constraint (gnomAD)

Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.

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ClinVar Variants

63 VUS of 74 total submissions

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Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

1.37LOEUF

pLI 0.000

Z-score 0.57

OE 0.83 (0.52–1.37)

Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?

0.05Z-score

OE missense 0.99 (0.86–1.13)

149 obs / 150.8 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.83 (0.52–1.37)

0≤0.351.4

Missense OE?0.99 (0.86–1.13)

0≤0.61.4

Synonymous OE?1.01

0≤1.21.6

LoF obs/exp: 11 / 13.3Missense obs/exp: 149 / 150.8Syn Z: -0.04

ClinVar Variant Classifications

74 submitted variants in ClinVar

ClinVar

Classification Summary

VUS63

Benign2

VUS

Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

Classification	Missense + Inframe	Synonymous	Total
Pathogenic	0	0	0
Likely Pathogenic	0	0	0
VUS	63	0	63
Likely Benign	0	0	0
Benign	1	1	2
Total	64	1	65

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

85 pathogenic / likely-pathogenic (of 97) ClinVar copy-number / structural variants overlap PDCD2 — these span large chromosomal regions, not the gene specifically, and are excluded from the counts above. Explore in CNV tools →