KCND1

potassium voltage-gated channel subfamily D member 1, the group of Potassium voltage-gated channels

Basic information

Region (hg38): X:48961377-48971844

Links

ENSG00000102057 ∙ NCBI:3750 ∙ OMIM:300281 ∙ HGNC:6237 ∙ Uniprot:Q9NSA2 ∙ 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 KCND1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KCND1 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				4	1	5
missense			19	1	2	22
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region			1			1
non coding						0
Total	0	0	19	5	3

Variants in KCND1

This is a list of pathogenic ClinVar variants found in the KCND1 region.

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

Position	Type	Phenotype	Significance	ClinVar
X-48962741-A-G		not specified	Uncertain significance (Dec 19, 2022)
X-48962751-G-A		Short stature • not specified	Uncertain significance (Jul 14, 2021)
X-48962803-A-G			Likely benign (Dec 31, 2019)
X-48966095-C-T		not specified	Uncertain significance (Feb 16, 2023)
X-48966157-C-T		not specified	Uncertain significance (Dec 06, 2022)
X-48966169-C-T		not specified	Uncertain significance (Jun 29, 2023)
X-48966182-A-C			Benign (Dec 20, 2018)
X-48966291-T-C			Likely benign (Jul 01, 2022)
X-48966313-C-A		Short stature	Likely pathogenic (Nov 18, 2001)
X-48966649-G-C			Benign (Dec 31, 2019)
X-48966670-C-T		not specified	Uncertain significance (Dec 03, 2021)
X-48966671-G-A			Benign (Dec 31, 2019)
X-48966826-T-C			Likely benign (Dec 31, 2019)
X-48966848-CAGAG-C			Uncertain significance (Mar 01, 2023)
X-48967057-T-C		not specified	Uncertain significance (Feb 21, 2024)
X-48967064-G-A			Likely benign (Jul 01, 2022)
X-48969361-T-C		not specified	Uncertain significance (Apr 26, 2024)
X-48969379-C-T		not specified	Uncertain significance (Jun 02, 2024)
X-48969499-C-T		not specified	Uncertain significance (Oct 26, 2021)
X-48969562-G-C		not specified	Uncertain significance (Feb 15, 2023)
X-48969669-G-A			Likely benign (Aug 01, 2022)
X-48969703-T-C		not specified	Uncertain significance (Oct 13, 2023)
X-48969760-C-T		not specified	Uncertain significance (May 03, 2024)
X-48969781-G-T		not specified	Uncertain significance (Dec 28, 2023)
X-48969916-G-A		not specified	Uncertain significance (Dec 07, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KCND1	protein_coding	protein_coding	ENST00000218176	6	9338

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.255	0.744	125728	4	5	125737	0.0000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.93	216	312	0.693	0.0000293	4181
Missense in Polyphen		60	107.02	0.56062		1461
Synonymous	0.583	122	130	0.935	0.0000122	1403
Loss of Function	2.83	4	16.3	0.245	0.00000140	226

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	0.000130	0.0000924
European (Non-Finnish)	0.0000494	0.0000352
Middle Eastern	0.00	0.00
South Asian	0.000165	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Pore-forming (alpha) subunit of voltage-gated rapidly inactivating A-type potassium channels. May contribute to I(To) current in heart and I(Sa) current in neurons. Channel properties are modulated by interactions with other alpha subunits and with regulatory subunits.
• Pathway: Neuronal System;Phase 1 - inactivation of fast Na+ channels;Cardiac conduction;Muscle contraction;Voltage gated Potassium channels;Potassium Channels (Consensus)

Recessive Scores

• pRec: 0.138

Intolerance Scores

• loftool: 0.0570
• rvis_EVS: -0.18
• rvis_percentile_EVS: 40.36

Haploinsufficiency Scores

• pHI: 0.471
• hipred: Y
• hipred_score: 0.707
• ghis: 0.519

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.307

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Kcnd1

Gene ontology

• Biological process: regulation of ion transmembrane transport;protein homooligomerization;potassium ion transmembrane transport
• Cellular component: cellular_component;plasma membrane;voltage-gated potassium channel complex;integral component of membrane;dendrite;neuronal cell body
• Molecular function: voltage-gated potassium channel activity;metal ion binding