ANAPC13

Chr 3

anaphase promoting complex subunit 13

Also known as: APC13, SWM1

NCBI Gene: 25847 ENSG00000129055 UniProt: Q9BS18 OMIM: 614484

This gene encodes a component of the anaphase promoting complex, a large ubiquitin-protein ligase that controls cell cycle progression by regulating the degradation of cell cycle regulators such as B-type cyclins. The encoded protein is evolutionarily conserved and is required for the integrity and ubiquitin ligase activity of the anaphase promoting complex. Pseudogenes and splice variants have been found for this gene; however, the biological validity of some of the splice variants has not been determined. [provided by RefSeq, Nov 2008]

OMIM Research

OMIM ResearchGenerating clinical summary…

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

1.86

LOEUF

GOF

Mechanism· predicted

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

1.86LOEUF

pLI 0.001

Z-score -0.12

OE 1.06 (0.50–1.86)

Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?

0.13Z-score

OE missense 0.94 (0.72–1.25)

36 obs / 38.2 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?1.06 (0.50–1.86)

0≤0.351.4

Missense OE?0.94 (0.72–1.25)

0≤0.61.4

Synonymous OE?1.16

0≤1.21.6

LoF obs/exp: 4 / 3.8Missense obs/exp: 36 / 38.2Syn Z: -0.46

Background carrier burden — how many people carry a rare variant somewhere in ANAPC13?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 1,600

80 rare PASS variants

Rare truncating (LoF)

1 in 7,700

19 rare PASS variants

Rare synonymous (reference)

1 in 1,000

33 rare PASS variants

Rare missense and truncating variants are carried at similar rates in ANAPC13; this gene does not show strong loss-of-function constraint by this measure. 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 1,900	1 in 6,900
South Asian	~43k	1 in 710	1 in 8,600
Remaining (unassigned)	~30k	1 in 1,400	≈ 1 in 15,000
European (Finnish)	~27k	1 in 1,400	none seen
Admixed American	~22k	1 in 1,600	≈ 1 in 22,000
African / African American	~21k	1 in 2,200	≈ 1 in 8,400
East Asian	~20k	1 in 660	≈ 1 in 6,600
Ashkenazi Jewish	~13k	≈ 1 in 4,400	≈ 1 in 13,000
Middle Eastern	~2,884	≈ 1 in 2,900	none seen

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): All 2 coding exons well covered in gnomAD exomes and genomes.? see exons ↓