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…

GOFmechanismLOEUF 1.86

Clinical Summary— ANAPC13

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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

10 VUS of 15 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?

1.86LOEUF

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

This gene — mechanism propensity

0.5869th %ile

GOF

0.87top 5%

LOF

0.3066th %ile

The highest-scoring mechanism for this gene is gain-of-function.

GOFprediction above median

Note: In-silico variant effect predictors (SIFT, PolyPhen, REVEL, CADD) may underestimate pathogenicity of missense variants in genes with GOF or DN mechanisms. Consider functional evidence and clinical context.

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312.

ClinVar Variant Classifications

15 submitted variants in ClinVar

ClinVar

Classification Summary

VUS10

VUS

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

Classification	Missense + Inframe	Total
Pathogenic	0	0
Likely Pathogenic	0	0
VUS	10	10
Likely Benign	0	0
Benign	0	0
Total	10	10

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

View in ClinVar →

18 pathogenic / likely-pathogenic (of 19) ClinVar copy-number / structural variants overlap ANAPC13 — these span large chromosomal regions, not the gene specifically, and are excluded from the counts above. Explore in CNV tools →