KCTD3

potassium channel tetramerization domain containing 3, the group of KCTD family|WD repeat domain containing

Basic information

Region (hg38): 1:215567304-215621807

Links

ENSG00000136636 ∙ NCBI:51133 ∙ OMIM:613272 ∙ HGNC:21305 ∙ Uniprot:Q9Y597 ∙ 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 KCTD3 gene.

• Inborn genetic diseases (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KCTD3 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	1	3
missense			21	3	1	25
nonsense	1					1
start loss						0
frameshift			3			3
inframe indel						0
splice donor/acceptor (+/-2bp)				1		1
splice region			2	1		3
non coding						0
Total	1	0	24	6	2

Variants in KCTD3

This is a list of pathogenic ClinVar variants found in the KCTD3 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-215567713-C-G		Inborn genetic diseases	Likely benign (Apr 07, 2023)
1-215573778-A-G			Likely benign (Jun 21, 2017)
1-215573799-A-G		Inborn genetic diseases	Uncertain significance (Mar 15, 2024)
1-215574078-T-C		Inborn genetic diseases	Uncertain significance (Nov 30, 2022)
1-215574102-G-A		Inborn genetic diseases	Uncertain significance (Apr 19, 2023)
1-215575952-CG-C		not specified	Uncertain significance (Jan 01, 2019)
1-215577722-C-T		Inborn genetic diseases	Uncertain significance (Nov 07, 2024)
1-215579011-C-G		Inborn genetic diseases	Uncertain significance (Sep 27, 2021)
1-215579080-C-G		Inborn genetic diseases	Uncertain significance (Aug 20, 2024)
1-215579080-C-T		Inborn genetic diseases	Uncertain significance (Aug 02, 2021)
1-215579093-C-T		Inborn genetic diseases	Uncertain significance (Oct 01, 2024)
1-215579114-C-T		Inborn genetic diseases	Uncertain significance (Nov 13, 2024)
1-215579122-G-A		Inborn genetic diseases	Uncertain significance (Oct 22, 2021)
1-215579905-A-G		Inborn genetic diseases	Uncertain significance (Mar 08, 2021)
1-215579927-G-A		Inborn genetic diseases	Uncertain significance (Mar 03, 2023)
1-215579962-A-G		Inborn genetic diseases	Uncertain significance (Mar 07, 2024)
1-215586516-G-A		Inborn genetic diseases	Pathogenic (Aug 08, 2022)
1-215586546-T-A		Inborn genetic diseases	Uncertain significance (Aug 16, 2022)
1-215586638-G-A		Inborn genetic diseases • KCTD3-related disorder	Likely benign (Sep 27, 2021)
1-215586653-G-A		KCTD3-related disorder	Uncertain significance (Jul 13, 2023)
1-215601885-A-G		Inborn genetic diseases	Uncertain significance (Nov 11, 2024)
1-215601930-A-T		Autism	Uncertain significance (Sep 05, 2022)
1-215602097-TCC-T		Autism, susceptibility to, 15	Uncertain significance (Mar 29, 2024)
1-215602098-CCCCTTGCGAATGAAAGATAATGATCTTCTTGTAACTGA-C		Congenital cerebellar hypoplasia;Seizure;Severe global developmental delay • Autism, susceptibility to, 15	Uncertain significance (Apr 04, 2024)
1-215602150-C-T		Inborn genetic diseases	Uncertain significance (Aug 12, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KCTD3	protein_coding	protein_coding	ENST00000259154	18	54415

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.101	0.899	125722	0	25	125747	0.0000994

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.76	263	422	0.623	0.0000217	5286
Missense in Polyphen		98	243.05	0.40321		2914
Synonymous	1.37	129	150	0.858	0.00000797	1607
Loss of Function	4.63	11	44.2	0.249	0.00000270	506

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000272	0.000272
Ashkenazi Jewish	0.00	0.00
East Asian	0.000218	0.000217
Finnish	0.0000925	0.0000924
European (Non-Finnish)	0.0000892	0.0000879
Middle Eastern	0.000218	0.000217
South Asian	0.0000988	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Accessory subunit of potassium/sodium hyperpolarization- activated cyclic nucleotide-gated channel 3 (HCN3) upregulating its cell-surface expression and current density without affecting its voltage dependence and kinetics. {ECO:0000250|UniProtKB:Q8BFX3}.

Recessive Scores

• pRec: 0.139

Intolerance Scores

• loftool: 0.586
• rvis_EVS: -0.67
• rvis_percentile_EVS: 15.76

Haploinsufficiency Scores

• pHI: 0.516
• hipred: Y
• hipred_score: 0.685
• ghis: 0.575

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.927

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Kctd3

Gene ontology

• Biological process: protein homooligomerization
• Cellular component: plasma membrane