KCTD13

Chr 16

potassium channel tetramerization domain containing 13

Also known as: BACURD1, FKSG86, PDIP1, POLDIP1, hBACURD1

NCBI Gene: 253980ENSG00000174943UniProt: Q8WZ19

Enables identical protein binding activity and small GTPase binding activity. Contributes to ubiquitin-protein transferase activity. Involved in several processes, including negative regulation of Rho protein signal transduction; proteasome-mediated ubiquitin-dependent protein catabolic process; and stress fiber assembly. Located in nuclear body. Part of Cul3-RING ubiquitin ligase complex. [provided by Alliance of Genome Resources, Jul 2025]

355
ClinVar variants
278
Pathogenic / LP
0.00
pLI score
0
Active trials
Clinical Summary— KCTD13
⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
278 Pathogenic / Likely Pathogenic· 54 VUS of 355 total submissions

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Tolerant — LoF & missense variants common in population
LoF Constraint?LOEUF (Loss-of-function Observed/Expected Upper bound Fraction) is the upper bound of the 90% CI for LoF OE — the preferred gnomAD v4 metric. Lower = more intolerant to LoF. LOEUF < 0.35 = highly constrained.
0.95LOEUF
pLI 0.001
Z-score 1.71
OE 0.51 (0.29–0.95)
Tolerant

Typical tolerance to LoF variation

Missense Constraint?Missense Z-score: standard deviations fewer missense variants observed vs. expected. Z > 3.09 (p < 0.001) = gene does not tolerate missense variation. OE missense < 0.6 is also considered constrained.
1.92Z-score
OE missense 0.63 (0.55–0.73)
138 obs / 217.7 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios?Shaded band = 90% confidence interval. Vertical tick = point estimate. Grey threshold line = gnomAD constraint cutoff for that variant class.
LoF OE?Ratio of observed to expected LoF variants. Upper CI bound (LOEUF) ≤ 0.35 = strong LoF constraint signal.0.51 (0.29–0.95)
0≤0.351.4
Missense OE?Ratio of observed to expected missense variants. OE ≤ 0.6 = fewer missense variants than expected by chance.0.63 (0.55–0.73)
0≤0.61.4
Synonymous OE?Control metric — synonymous variants are largely neutral and expected near OE = 1.0. Significant deviation may indicate annotation issues.0.93
0≤1.21.6
LoF obs/exp: 7 / 13.9Missense obs/exp: 138 / 217.7Syn Z: 0.52

ClinVar Variant Classifications

355 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic235
Likely Pathogenic43
VUS54
Likely Benign3
235
Pathogenic
43
Likely Pathogenic
54
VUS
3
Likely Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
235
0
235
Likely Pathogenic
0
0
43
0
43
VUS
0
40
14
0
54
Likely Benign
0
0
1
2
3
Benign
0
0
0
0
0
Total0402932335

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

View in ClinVar →

Protein Context — Lollipop Plot

KCTD13 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

OMIM — Genotype-Phenotype Relationships

1 OMIM entry

OMIM
Clinical Literature
Landmark / reviewRecent case evidence
Key Publications
Landmark & review papers · by relevance
PubMed
Gene dosage changes in KCTD13 result in penile and testicular anomalies via diminished androgen receptor function.
Seth A et al.·FASEB J
2022
Identification of rare variants in KCTD13 at the schizophrenia risk locus 16p11.2.
Degenhardt F et al.·Psychiatr Genet
2016
KCTD13 is a major driver of mirrored neuroanatomical phenotypes of the 16p11.2 copy number variant.
Golzio C et al.·Nature
2012
A Potential Contributory Role for Ciliary Dysfunction in the 16p11.2 600 kb BP4-BP5 Pathology.
Migliavacca E et al.·Am J Hum Genet
2015
Identification of genetic loci that overlap between schizophrenia and metabolic syndrome.
Lv H et al.·Psychiatry Res
2022
STK25 and MST3 Have Overlapping Roles to Regulate Rho GTPases during Cortical Development.
Matsuki T et al.·J Neurosci
2021
Microdeletion and microduplication syndromes, including recurrent rearrangements at 16p11.2 and 22q11.21, are enriched in unexplained male infertility.
Kikas T et al.·Hum Reprod
2026
Genomic and Reverse Translational Analysis Discloses a Role for Small GTPase RhoA Signaling in the Pathogenesis of Schizophrenia: Rho-Kinase as a Novel Drug Target.
Tanaka R et al.·Int J Mol Sci
2023Review
The effect of copy number variations in chromosome 16p on body weight in patients with intellectual disability.
Gimeno-Ferrer F et al.·J Hum Genet
2019Cohort
The Immune Signaling Adaptor LAT Contributes to the Neuroanatomical Phenotype of 16p11.2 BP2-BP3 CNVs.
Loviglio MN et al.·Am J Hum Genet
2017
Top 10 resultsSearch PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
Top 5 resultsSearch Europe PMC ↗

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →

External Resources

Links to major genomics databases and tools