KCTD12

potassium channel tetramerization domain containing 12, the group of KCTD family

Basic information

Region (hg38): 13:76880174-76886405

Previous symbols: [ "C13orf2" ]

Links

ENSG00000178695 ∙ NCBI:115207 ∙ OMIM:610521 ∙ HGNC:14678 ∙ Uniprot:Q96CX2 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the KCTD12 gene.

• Inborn genetic diseases (7 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KCTD12 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous					2	2
missense			7			7
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	7	0	2

Variants in KCTD12

This is a list of pathogenic ClinVar variants found in the KCTD12 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
13-76885276-C-T		not specified	Uncertain significance (Feb 17, 2023)
13-76885290-A-C		not specified	Uncertain significance (Apr 07, 2023)
13-76885367-C-A		not specified	Uncertain significance (Dec 22, 2023)
13-76885468-G-C		not specified	Uncertain significance (Jan 02, 2024)
13-76885480-G-T		not specified	Uncertain significance (Oct 27, 2022)
13-76885513-G-C		not specified	Uncertain significance (Oct 24, 2023)
13-76885543-G-C		not specified	Uncertain significance (Jan 02, 2024)
13-76885553-T-A		not specified	Uncertain significance (Dec 19, 2022)
13-76885692-C-T		not specified	Uncertain significance (Jan 05, 2022)
13-76885888-G-A			Benign (Jul 03, 2018)
13-76885922-C-T		not specified	Uncertain significance (Jul 19, 2023)
13-76885945-C-T			Benign (Jun 18, 2018)
13-76886076-A-T		not specified	Uncertain significance (Dec 06, 2022)
13-76886127-G-C		not specified	Uncertain significance (Jul 19, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KCTD12	protein_coding	protein_coding	ENST00000377474	1	6229

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0617	0.876	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.762	145	173	0.837	0.00000794	2011
Missense in Polyphen		28	57.176	0.48971		628
Synonymous	-2.54	112	82.6	1.36	0.00000403	703
Loss of Function	1.57	3	7.69	0.390	3.29e-7	89

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Auxiliary subunit of GABA-B receptors that determine the pharmacology and kinetics of the receptor response. Increases agonist potency and markedly alter the G-protein signaling of the receptors by accelerating onset and promoting desensitization (By similarity). {ECO:0000250}.

Recessive Scores

• pRec: 0.129

Haploinsufficiency Scores

• pHI: 0.776
• hipred: N
• hipred_score: 0.468
• ghis: 0.554

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.834

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Kctd12
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan)

Zebrafish Information Network

• Gene name: kctd12.2
• Affected structure: ventral habenular nucleus
• Phenotype tag: abnormal
• Phenotype quality: increased volume

Gene ontology

• Biological process: protein homooligomerization
• Cellular component: cell junction;presynaptic membrane;postsynaptic membrane
• Molecular function: RNA binding;identical protein binding