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 (66 variants)
• not_provided (10 variants)
• KCTD3-related_disorder (4 variants)
• Autism,_susceptibility_to,_15 (2 variants)
• Autism (1 variants)
• Congenital_cerebellar_hypoplasia (1 variants)
• not_specified (1 variants)
• Seizure (1 variants)
• Severe_global_developmental_delay (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. These statistics are base on transcript: NM_000016121.5. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				2	1	3
missense			63	4	1	68
nonsense	1		1			2
start loss						0
frameshift			4			4
splice donor/acceptor (+/-2bp)				1		1
Total	1	0	68	7	2

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