KXD1

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			29 clinvar	2 clinvar		31
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	30	2	0	32

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 104 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_024069.4	RefSeq	NP_076974.2	4	MANE Select
ENST00000222307.9	Ensembl	ENSP00000222307.3	4	MANE Select
NM_001171948.2	RefSeq	NP_001165419.1	4	Standard
NM_001171949.2	RefSeq	NP_001165420.1	4	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

vesicle-mediated transport
lysosome localization

Molecular Function

protein binding

Cellular Component

lysosomal membrane
BLOC-1 complex
BORC complex

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000602094
Coding exons: 4
Length: 11626
Individuals with no LoFs: 125458
Homozygous LoFs: 0
Heterozygous LoFs: 5
Defined: 125463
p: 0.0000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.899	88	115	0.764	0.00000744	1161
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000027	0.000026	rare
South Asian	0.000067	0.000065	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.114

Gene Damage Prediction

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