KCTD17

potassium channel tetramerization domain containing 17, the group of KCTD family

Basic information

Region (hg38): 22:37051738-37063390

Links

ENSG00000100379 ∙ NCBI:79734 ∙ OMIM:616386 ∙ HGNC:25705 ∙ Uniprot:Q8N5Z5 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• myoclonic dystonia 26 (Limited), mode of inheritance: AD
• myoclonic dystonia 26 (Strong), mode of inheritance: AD
• myoclonus-dystonia syndrome (Supportive), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Dystonia 26, myoclonic	AD	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Neurologic	25983243
Surgery with pallidal deep brain stimulation has been described as beneficial, though the impact of early diagnosis is unclear

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the KCTD17 gene.

• Myoclonic dystonia 26 (88 variants)
• not provided (33 variants)
• Inborn genetic diseases (15 variants)
• not specified (1 variants)
• KCTD17-related condition (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KCTD17 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				24	4	28
missense	1		42	4	1	48
nonsense			1			1
start loss			1			1
frameshift	1					1
inframe indel			1			1
splice donor/acceptor (+/-2bp)			1			1
splice region			2	3	1	6
non coding			2	23	9	34
Total	2	0	48	51	14

Variants in KCTD17

This is a list of pathogenic ClinVar variants found in the KCTD17 region.

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

Position	Type	Phenotype	Significance	ClinVar
22-37051746-A-C		Inborn genetic diseases	Uncertain significance (Oct 12, 2022)
22-37051750-C-G		Myoclonic dystonia 26	Uncertain significance (Nov 12, 2022)
22-37051751-G-A		Myoclonic dystonia 26	Likely benign (Aug 07, 2021)
22-37051756-C-A		Inborn genetic diseases	Uncertain significance (Nov 30, 2022)
22-37051761-A-T			Uncertain significance (Oct 01, 2023)
22-37051765-G-C		Myoclonic dystonia 26	Uncertain significance (Oct 21, 2019)
22-37051766-G-C		Myoclonic dystonia 26	Uncertain significance (Mar 26, 2022)
22-37051777-G-A		Myoclonic dystonia 26	Uncertain significance (Sep 04, 2021)
22-37051778-G-C		Myoclonic dystonia 26	Likely benign (Sep 24, 2022)
22-37051780-A-G		Myoclonic dystonia 26	Uncertain significance (Jun 27, 2022)
22-37051792-C-T		Inborn genetic diseases	Uncertain significance (Nov 01, 2022)
22-37051800-G-T		Myoclonic dystonia 26	Uncertain significance (Apr 26, 2023)
22-37051801-C-T		Myoclonic dystonia 26	Uncertain significance (Dec 16, 2023)
22-37051802-G-A		Myoclonic dystonia 26	Likely benign (Jun 21, 2023)
22-37051802-G-T		Myoclonic dystonia 26	Likely benign (Feb 24, 2023)
22-37051815-G-A		Myoclonic dystonia 26 • KCTD17-related disorder	Benign (Jan 30, 2024)
22-37051816-C-T		Inborn genetic diseases	Uncertain significance (May 17, 2023)
22-37051817-A-C		Myoclonic dystonia 26	Likely benign (Jan 25, 2024)
22-37051850-G-C		Myoclonic dystonia 26	Likely benign (Jul 19, 2022)
22-37051853-G-A		Myoclonic dystonia 26	Likely benign (Jan 22, 2020)
22-37051859-G-A		Myoclonic dystonia 26	Benign/Likely benign (Dec 22, 2023)
22-37051883-G-A		Myoclonic dystonia 26	Likely benign (Jan 27, 2023)
22-37051904-C-T		Myoclonic dystonia 26	Likely benign (Dec 01, 2023)
22-37051968-G-A		Myoclonic dystonia 26	Likely benign (Feb 28, 2022)
22-37051980-C-T			Likely benign (Apr 19, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KCTD17	protein_coding	protein_coding	ENST00000402077	8	11652

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0177	0.963	125538	0	7	125545	0.0000279

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.58	99	154	0.642	0.00000948	1899
Missense in Polyphen		16	44.618	0.3586		459
Synonymous	-0.133	62	60.7	1.02	0.00000384	555
Loss of Function	2.04	5	12.9	0.387	5.50e-7	176

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000585	0.0000585
Ashkenazi Jewish	0.00	0.00
East Asian	0.000113	0.000109
Finnish	0.0000465	0.0000462
European (Non-Finnish)	0.0000182	0.0000176
Middle Eastern	0.000113	0.000109
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Is a positive regulator of ciliogenesis, playing a crucial role in the initial steps of axoneme extension. It acts as a substrate-adapter for CUL3-RING ubiquitin ligase complexes which mediate the ubiquitination and subsequent proteasomal degradation of TCHP, a protein involved in ciliogenesis down-regulation (PubMed:25270598). May be involved in endoplasmic reticulum calcium ion homeostasis (PubMed:25983243). {ECO:0000269|PubMed:25270598, ECO:0000269|PubMed:25983243}.

Recessive Scores

• pRec: 0.108

Intolerance Scores

• loftool: 0.460
• rvis_EVS: 0.08
• rvis_percentile_EVS: 60.09

Haploinsufficiency Scores

• pHI: 0.128
• hipred: N
• hipred_score: 0.339
• ghis: 0.580

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.800

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Kctd17

Gene ontology

• Biological process: cell projection organization;endoplasmic reticulum calcium ion homeostasis;proteasome-mediated ubiquitin-dependent protein catabolic process;positive regulation of cilium assembly;protein homooligomerization
• Cellular component: cytoplasm;endoplasmic reticulum;Cul3-RING ubiquitin ligase complex
• Molecular function: protein binding;identical protein binding;cullin family protein binding