KXD1

KxDL motif containing 1, the group of BLOC-1 related complex subunits

Basic information

Region (hg38): 19:18557762-18569387

Previous symbols: [ "C19orf50" ]

Links

ENSG00000105700 ∙ NCBI:79036 ∙ OMIM:615178 ∙ HGNC:28420 ∙ Uniprot:Q9BQD3 ∙ 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 KXD1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KXD1 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						0
missense			8	2		10
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	8	2	0

Variants in KXD1

This is a list of pathogenic ClinVar variants found in the KXD1 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-18562093-G-A		not specified	Likely benign (Mar 21, 2023)
19-18562125-T-A			not provided (-)
19-18564886-A-G		not specified	Uncertain significance (Oct 09, 2024)
19-18564948-G-A		not specified	Uncertain significance (Jan 23, 2024)
19-18564991-G-A		not specified	Uncertain significance (Feb 24, 2022)
19-18565002-A-G		not specified	Uncertain significance (May 01, 2022)
19-18565015-G-A		not specified	Uncertain significance (Nov 13, 2024)
19-18567134-C-T		not specified	Uncertain significance (Aug 27, 2024)
19-18568492-C-T		not specified	Uncertain significance (Nov 25, 2024)
19-18568521-G-A		not specified	Uncertain significance (Nov 25, 2024)
19-18568537-G-T		not specified	Uncertain significance (Dec 19, 2022)
19-18568542-G-A		not specified	Uncertain significance (Jun 22, 2021)
19-18568564-T-G		not specified	Uncertain significance (Oct 03, 2023)
19-18568593-C-T		not specified	Uncertain significance (Jul 17, 2024)
19-18568594-G-A		not specified	Likely benign (Feb 15, 2023)
19-18568603-C-G		not specified	Uncertain significance (Jul 09, 2021)
19-18568618-T-G		not specified	Uncertain significance (Jul 20, 2021)
19-18568621-C-T		not specified	Uncertain significance (Aug 28, 2024)
19-18568623-G-C		not specified	Uncertain significance (Aug 12, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KXD1	protein_coding	protein_coding	ENST00000602094	4	11626

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0349	0.838	125458	0	5	125463	0.0000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.899	88	115	0.764	0.00000744	1161
Missense in Polyphen		21	31.02	0.67697		341
Synonymous	-0.0425	50	49.6	1.01	0.00000358	346
Loss of Function	1.21	3	6.28	0.478	3.68e-7	65

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)	0.0000275	0.0000265
Middle Eastern	0.00	0.00
South Asian	0.0000669	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: As part of the BORC complex may play a role in lysosomes movement and localization at the cell periphery. Associated with the cytosolic face of lysosomes, the BORC complex may recruit ARL8B and couple lysosomes to microtubule plus-end-directed kinesin motor (PubMed:25898167). May be involved in the biogenesis of lysosome-related organelles such as melanosomes (By similarity). {ECO:0000250|UniProtKB:Q80XH1, ECO:0000269|PubMed:25898167}.

Recessive Scores

• pRec: 0.111

Intolerance Scores

• rvis_EVS: 0.57
• rvis_percentile_EVS: 81.99

Haploinsufficiency Scores

• pHI: 0.186
• hipred: N
• hipred_score: 0.297
• ghis: 0.414

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Kxd1
• Phenotype: pigmentation phenotype; hematopoietic system phenotype; vision/eye phenotype

Gene ontology

• Biological process: vesicle-mediated transport;lysosome localization
• Cellular component: lysosomal membrane;BLOC-1 complex;BORC complex
• Molecular function: protein binding