PDCD7

Chr 15

programmed cell death 7

Also known as: 59K, ES18, HES18

NCBI Gene: 10081 ENSG00000090470 UniProt: Q8N8D1 OMIM: 608138

This gene encodes a 59 kDa protein that is associated with the U11 small nuclear ribonucleoprotein (snRNP), which is a component of the minor U12-type spliceosome responsible for catalyzing pre-mRNA splicing of U12-type introns. [provided by RefSeq, Dec 2010]

OMIM Research

OMIM ResearchGenerating clinical summary…

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

1.12

LOEUF

GOF

Mechanism· predicted

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

1.12LOEUF

pLI 0.000

Z-score 1.22

OE 0.66 (0.41–1.12)

Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?

0.75Z-score

OE missense 0.84 (0.74–0.96)

153 obs / 181.5 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.66 (0.41–1.12)

0≤0.351.4

Missense OE?0.84 (0.74–0.96)

0≤0.61.4

Synonymous OE?0.88

0≤1.21.6

LoF obs/exp: 10 / 15.1Missense obs/exp: 153 / 181.5Syn Z: 0.83

Background carrier burden — how many people carry a rare variant somewhere in PDCD7?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 96

711 rare PASS variants

Rare truncating (LoF)

1 in 1,200

114 rare PASS variants

Rare synonymous (reference)

1 in 200

319 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for PDCD7. A background rate for each class, not the frequency of any particular variant; thin-coverage exons undercount.

By genetic ancestry · 9 gnomAD groups · rare = under 0.1% in that group

Group	People	Missense	Truncating
European (non-Finnish)	~556k	1 in 150	1 in 1,200
South Asian	~43k	1 in 62	1 in 730
Remaining (unassigned)	~30k	1 in 100	1 in 1,100
European (Finnish)	~27k	1 in 150	1 in 960
Admixed American	~22k	1 in 110	1 in 1,400
African / African American	~21k	1 in 67	1 in 1,200
East Asian	~20k	1 in 110	1 in 2,000
Ashkenazi Jewish	~13k	1 in 280	≈ 1 in 4,600
Middle Eastern	~2,884	1 in 130	≈ 1 in 910

Each group is summed over the variants that are rare in that group. Grey ≈ figures rest on fewer than five expected carriers — too few to distinguish groups. Differences mostly reflect how many people were sampled and how much variation each ancestry carries, not disease risk.

Exome coverage (gnomAD): 4 of 5 coding exons well covered in gnomAD exomes; exon 1 marginal. Genomes: all 5.? see exons ↓