KXD1

Summary

KXD1 (KxDL motif containing 1, HGNC:28420) is a protein-coding gene on chromosome 19p13.11, encoding KxDL motif-containing protein 1 (Q9BQD3). As part of the BORC complex may play a role in lysosomes movement and localization at the cell periphery.

Involved in lysosome localization. Part of BORC complex.

Source: NCBI Gene 79036 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 37 total
• MANE Select transcript: NM_024069

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:28420
Approved symbol	KXD1
Name	KxDL motif containing 1
Location	19p13.11
Locus type	gene with protein product
Status	Approved
Aliases	FLJ25480, MGC2749, KXDL, BORCS4
Ensembl gene	ENSG00000105700
Ensembl biotype	protein_coding
OMIM	615178
Entrez	79036

Gene structure

Transcript identifiers

Ensembl transcripts: 55 — 53 protein_coding, 1 nonsense_mediated_decay, 1 protein_coding_CDS_not_defined

ENST00000222307, ENST00000539106, ENST00000540691, ENST00000595073, ENST00000595870, ENST00000596244, ENST00000596785, ENST00000597438, ENST00000598830, ENST00000599000, ENST00000599319, ENST00000600099, ENST00000600372, ENST00000600654, ENST00000600796, ENST00000601630, ENST00000602094, ENST00000859406, ENST00000859407, ENST00000859408, ENST00000859409, ENST00000859410, ENST00000859411, ENST00000859412, ENST00000859413, ENST00000859414, ENST00000859415, ENST00000859416, ENST00000859417, ENST00000859418, ENST00000859419, ENST00000859420, ENST00000859421, ENST00000859422, ENST00000859423, ENST00000916832, ENST00000916833, ENST00000916834, ENST00000916835, ENST00000916836, ENST00000916837, ENST00000916838, ENST00000916839, ENST00000916840, ENST00000916841, ENST00000916842, ENST00000916843, ENST00000916844, ENST00000970587, ENST00000970588, ENST00000970589, ENST00000970590, ENST00000970591, ENST00000970592, ENST00000970593

RefSeq mRNA: 3 — MANE Select: NM_024069 NM_001171948, NM_001171949, NM_024069

CCDS: CCDS12381

Canonical transcript exons

ENST00000222307 — 5 exons

Exon	Start	End
ENSE00000691175	18567132	18567178
ENSE00000691177	18564869	18565021
ENSE00000691179	18562036	18562157
ENSE00003041479	18557870	18557914
ENSE00003190256	18568402	18569378

Expression profiles

Bgee: expression breadth ubiquitous, 282 present calls, max score 97.32.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 135.2630 / max 1407.2220, expressed in 1828 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter ID	TPM avg	Samples expressed
174685	70.4871	1827
174682	44.0566	1814
174684	12.1969	1806
174683	7.9062	1757
174686	0.6161	273

Top tissues by expression

295 total, by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
right coronary artery	UBERON:0001625	97.32	gold quality
popliteal artery	UBERON:0002250	97.27	gold quality
tibial artery	UBERON:0007610	97.27	gold quality
lower esophagus	UBERON:0013473	97.17	gold quality
lower esophagus muscularis layer	UBERON:0035833	97.17	gold quality
ascending aorta	UBERON:0001496	97.15	gold quality
aorta	UBERON:0000947	97.14	gold quality
thoracic aorta	UBERON:0001515	97.14	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	97.13	gold quality
nerve	UBERON:0001021	97.09	gold quality
tibial nerve	UBERON:0001323	97.09	gold quality
descending thoracic aorta	UBERON:0002345	97.04	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	96.96	gold quality
left coronary artery	UBERON:0001626	96.95	gold quality
granulocyte	CL:0000094	96.90	gold quality
muscle layer of sigmoid colon	UBERON:0035805	96.81	gold quality
mucosa of stomach	UBERON:0001199	96.66	gold quality
adenohypophysis	UBERON:0002196	96.59	gold quality
body of pancreas	UBERON:0001150	96.55	gold quality
stromal cell of endometrium	CL:0002255	96.50	gold quality
coronary artery	UBERON:0001621	96.48	gold quality
monocyte	CL:0000576	96.44	gold quality
lower esophagus mucosa	UBERON:0035834	96.40	gold quality
right testis	UBERON:0004534	96.39	gold quality
body of stomach	UBERON:0001161	96.36	gold quality
left ovary	UBERON:0002119	96.33	gold quality
left testis	UBERON:0004533	96.31	gold quality
body of uterus	UBERON:0009853	96.25	gold quality
endocervix	UBERON:0000458	96.24	gold quality
mononuclear cell	CL:0000842	96.15	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-MTAB-6379	no	535.23
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

33 targeting KXD1, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-30A-5P	100.00	76.31	3233
HSA-MIR-30B-5P	100.00	76.29	3248
HSA-MIR-30C-5P	100.00	76.29	3248
HSA-MIR-30D-5P	100.00	76.32	3233
HSA-MIR-30E-5P	100.00	76.32	3242
HSA-MIR-6744-5P	99.93	66.82	748
HSA-MIR-12119	99.87	68.35	1653
HSA-MIR-3919	99.87	69.45	2489
HSA-MIR-6124	99.87	69.78	3551
HSA-MIR-5003-3P	99.85	69.29	2517
HSA-MIR-204-5P	99.79	71.62	2439
HSA-MIR-211-5P	99.79	71.65	2440
HSA-MIR-623	99.76	68.16	1170
HSA-MIR-4446-5P	99.72	69.19	2544
HSA-MIR-4755-5P	99.71	70.34	2716
HSA-MIR-5006-3P	99.71	70.26	2728
HSA-MIR-6832-3P	99.52	70.44	1726
HSA-MIR-486-3P	99.51	66.82	1901
HSA-MIR-3064-5P	99.26	66.13	1497
HSA-MIR-3085-3P	99.26	66.16	1490
HSA-MIR-6504-5P	99.26	65.95	1487
HSA-MIR-149-5P	99.25	67.16	1315
HSA-MIR-4711-3P	98.97	66.87	1020
HSA-MIR-4656	98.79	66.22	1306
HSA-MIR-340-3P	98.11	68.25	679
HSA-MIR-6827-3P	98.08	72.27	651
HSA-MIR-3173-5P	97.35	65.82	1282
HSA-MIR-6799-3P	97.35	65.60	1302
HSA-MIR-6859-3P	97.26	64.69	428
HSA-MIR-505-5P	97.01	65.54	778

Literature-anchored findings (GeneRIF, showing 2)

• KXD1 interacts with BLOS1. (PMID:22554196)
• BORC complex specific components and Kinesin-1 mediate autophagy evasion by the autophagy-resistant Mycobacterium tuberculosis Beijing strain. (PMID:36717601)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	kxd1	ENSDARG00000051934
mus_musculus	Kxd1	ENSMUSG00000055553
rattus_norvegicus	Kxd1	ENSRNOG00000019971
drosophila_melanogaster	CG10681	FBGN0036291
caenorhabditis_elegans		WBGENE00015742

Protein

Protein identifiers

KxDL motif-containing protein 1 — Q9BQD3 (reviewed: Q9BQD3)

All UniProt accessions (8): Q9BQD3, M0QX74, M0QXN9, M0QXP3, M0QY77, M0R0B4, M0R228, M0R2G3

UniProt curated annotations — full annotation on UniProt →

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. May be involved in the biogenesis of lysosome-related organelles such as melanosomes.

Subunit / interactions. Component of the BLOC-one-related complex (BORC) which is composed of BLOC1S1, BLOC1S2, BORCS5, BORCS6, BORCS7, BORCS8, KXD1 and SNAPIN. Associates with the BLOC-1 complex. Interacts with BLOC1S1. Interacts with DTNBP1/BLOC1S7 (via coiled-coil domain).

Subcellular location. Lysosome membrane.

Similarity. Belongs to the KXD1 family.

RefSeq proteins (3): NP_001165419, NP_001165420, NP_076974* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR019371	KxDL_dom	Domain
IPR039843	KXD1-like	Family

Pfam: PF10241

UniProt features (6 total): compositionally biased region 2, chain 1, region of interest 1, modified residue 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9BQD3-F1	77.02	0.51

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Post-translational modifications (1): 1

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 192 (showing top): MORF_DNMT1, GOCC_VACUOLAR_MEMBRANE, MORF_SNRP70, STARK_PREFRONTAL_CORTEX_22Q11_DELETION_DN, MORF_UBE2I, MORF_HDAC1, MORF_UBE2N, MORF_CDK2, MORF_HDAC2, GOBP_VESICLE_MEDIATED_TRANSPORT, GOBP_ORGANELLE_TRANSPORT_ALONG_MICROTUBULE, MORF_TERF1, GOBP_REGULATION_OF_ANATOMICAL_STRUCTURE_SIZE, MORF_SKP1A, MORF_RAF1

GO Biological Process (5): vesicle-mediated transport (GO:0016192), lysosome localization (GO:0032418), regulation of endosome size (GO:0051036), regulation of lysosome size (GO:0062196), organelle transport along microtubule (GO:0072384)

GO Molecular Function (1): protein binding (GO:0005515)

GO Cellular Component (6): cytoplasmic side of lysosomal membrane (GO:0098574), BORC complex (GO:0099078), lysosome (GO:0005764), lysosomal membrane (GO:0005765), membrane (GO:0016020), BLOC-1 complex (GO:0031083)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
transport	1
cellular process	1
vacuolar localization	1
regulation of vesicle size	1
regulation of cellular component size	1
transport along microtubule	1
establishment of organelle localization	1
binding	1
lysosomal membrane	1
cytoplasmic side of membrane	1
intracellular protein-containing complex	1
lytic vacuole	1
lysosome	1
lytic vacuole membrane	1
cellular anatomical structure	1
BLOC complex	1

Protein interactions and networks

STRING

707 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
KXD1	BORCS6	Q96GS4	995
KXD1	BLOC1S1	P78537	991
KXD1	BORCS5	Q969J3	990
KXD1	BLOC1S2	Q6QNY1	989
KXD1	SNAPIN	O95295	988
KXD1	BORCS7	Q96B45	987
KXD1	BORCS8	Q96FH0	985
KXD1	ARL8B	Q9NVJ2	677
KXD1	ARL8A	Q96BM9	634
KXD1	ARL5B	Q96KC2	606
KXD1	BLOC1S6	Q9UL45	543
KXD1	DDX49	Q9Y6V7	492
KXD1	AP3M1	Q9Y2T2	475
KXD1	TMEM59L	Q9UK28	466
KXD1	PGPEP1	Q9NXJ5	455

IntAct

201 interactions, top by confidence:

A	B	Type	Score
LAMTOR4	LAMTOR5	psi-mi:“MI:0914”(association)	0.960
KXD1	TPM3	psi-mi:“MI:0915”(physical association)	0.920
TPM3	KXD1	psi-mi:“MI:0915”(physical association)	0.920
BLOC1S1	SNAPIN	psi-mi:“MI:0914”(association)	0.810
KXD1	TPM1	psi-mi:“MI:0915”(physical association)	0.800
TPM1	KXD1	psi-mi:“MI:0915”(physical association)	0.800
BORCS6	KXD1	psi-mi:“MI:0915”(physical association)	0.800
EXOC3	EXOC5	psi-mi:“MI:0914”(association)	0.790
KXD1	CEP19	psi-mi:“MI:0915”(physical association)	0.780
CEP19	KXD1	psi-mi:“MI:0915”(physical association)	0.780
IFT20	KXD1	psi-mi:“MI:0915”(physical association)	0.770
KXD1	IFT20	psi-mi:“MI:0915”(physical association)	0.770
TPM1	KXD1	psi-mi:“MI:0915”(physical association)	0.740

BioGRID (234): KXD1 (Two-hybrid), KXD1 (Two-hybrid), KXD1 (Two-hybrid), KXD1 (Two-hybrid), KXD1 (Two-hybrid), KXD1 (Two-hybrid), KXD1 (Two-hybrid), MAP1LC3B (Two-hybrid), MAP1LC3A (Two-hybrid), CEP19 (Two-hybrid), IFT20 (Two-hybrid), HAUS1 (Two-hybrid), ZNF417 (Two-hybrid), LRRC45 (Two-hybrid), C4orf46 (Two-hybrid)

ESM2 similar proteins: A0JPN6, A4IIZ9, A5WUL3, A8E5U3, F1R7R1, F4HPA7, F4HRV8, O43513, O57595, O75934, P61289, P61290, P61291, Q15528, Q2F7Z4, Q2TBN4, Q2YDF2, Q3B8I4, Q3T123, Q4R4V3, Q5BJ48, Q5E9K2, Q5F3J5, Q5PPY2, Q5RFD3, Q5RHQ8, Q5RKN3, Q5XIX8, Q5ZKF4, Q62276, Q62717, Q62739, Q68EF0, Q6GLR7, Q6GPR9, Q6GQ95, Q7ZV35, Q800L3, Q80TJ1, Q86UW7

Diamond homologs: A2XK00, Q0V9C8, Q3SZV2, Q5M853, Q6ASS9, Q6DBR9, Q6DDT0, Q80XH1, Q9BQD3, Q9VTY4

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 104 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

Pathway	Partners	Fold	FDR
Autophagy	6	14.3×	5e-04
Macroautophagy	7	13.0×	3e-04
Translocation of SLC2A4 (GLUT4) to the plasma membrane	5	12.4×	3e-03

GO biological processes:

GO term	Partners	Fold	FDR
lysosome localization	7	42.9×	1e-07
exocytosis	6	10.6×	9e-04

Disease & clinical

Clinical variants and AI predictions

ClinVar

37 variants total. Per-class counts are floors (≥ shown; pagination cap):

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	27
Likely benign	2
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1021 predictions. Top by Δscore:

Variant	Effect	Δscore
19:18562028:T:TA	acceptor_gain	1.0000
19:18562031:TTCA:T	acceptor_loss	1.0000
19:18562033:CA:C	acceptor_loss	1.0000
19:18562034:A:AG	acceptor_gain	1.0000
19:18562034:A:T	acceptor_loss	1.0000
19:18562035:G:A	acceptor_loss	1.0000
19:18562035:G:GT	acceptor_gain	1.0000
19:18562035:GGC:G	acceptor_gain	1.0000
19:18562035:GGCA:G	acceptor_gain	1.0000
19:18562153:AACAT:A	donor_gain	1.0000
19:18562154:ACAT:A	donor_gain	1.0000
19:18562155:CAT:C	donor_gain	1.0000
19:18562155:CATGT:C	donor_loss	1.0000
19:18562156:AT:A	donor_gain	1.0000
19:18562158:G:GG	donor_gain	1.0000
19:18564861:A:AG	acceptor_gain	1.0000
19:18564862:C:G	acceptor_gain	1.0000
19:18564864:A:AG	acceptor_gain	1.0000
19:18564864:ATCAG:A	acceptor_gain	1.0000
19:18564865:TCA:T	acceptor_loss	1.0000
19:18564866:CA:C	acceptor_loss	1.0000
19:18564867:A:AC	acceptor_loss	1.0000
19:18564867:A:AG	acceptor_gain	1.0000
19:18564867:AG:A	acceptor_gain	1.0000
19:18564867:AGGCT:A	acceptor_gain	1.0000
19:18564868:G:GA	acceptor_gain	1.0000
19:18564868:GG:G	acceptor_gain	1.0000
19:18564868:GGC:G	acceptor_gain	1.0000
19:18564868:GGCT:G	acceptor_gain	1.0000
19:18564868:GGCTG:G	acceptor_gain	1.0000

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000428222 (19:18559522 A>G), RS1000428428 (19:18563628 C>G), RS1000520443 (19:18567483 T>C), RS1000927359 (19:18556923 C>A,T), RS1000954637 (19:18567669 C>T), RS1001025787 (19:18562648 G>A), RS1001232945 (19:18557824 C>T), RS1001358517 (19:18557546 C>T), RS1001472505 (19:18566687 G>A), RS1001754503 (19:18568296 A>C,G), RS1001829954 (19:18556664 T>A,C), RS1002205600 (19:18562228 C>T), RS1002517553 (19:18559105 A>G), RS1002642520 (19:18556177 C>A,T), RS1003194322 (19:18567741 C>T)

Disease associations

OMIM: gene MIM:615178 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

19 total (human), top 19 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Air Pollutants	increases abundance, increases oxidation, affects expression, affects cotreatment	2
Ozone	affects cotreatment, increases oxidation, increases abundance, affects expression	2
Valproic Acid	decreases expression, increases methylation	2
dicrotophos	increases expression	1
triphenyl phosphate	affects expression	1
alpha-pinene	affects cotreatment, increases oxidation, increases abundance	1
beta-lapachone	decreases expression	1
methacrylaldehyde	increases oxidation, increases abundance, affects cotreatment	1
jinfukang	increases expression	1
(+)-JQ1 compound	decreases expression	1
Temozolomide	increases expression	1
Acrolein	affects cotreatment, increases oxidation, increases abundance	1
Vehicle Emissions	decreases expression, increases abundance	1
Benzo(a)pyrene	affects methylation, decreases methylation	1
Doxorubicin	increases expression	1
Smoke	decreases expression	1
Cyclosporine	increases expression	1
Particulate Matter	decreases expression, increases abundance	1
Volatile Organic Compounds	affects cotreatment, increases oxidation	1

Cellosaurus cell lines

3 cell lines: 2 cancer cell line, 1 transformed cell line

First 10 cell lines (id-ordered, not curated):

Cellosaurus	Name	Category	Sex
CVCL_B2ZY	Abcam HEK293T KXD1 KO	Transformed cell line	Female
CVCL_SV16	HAP1 KXD1 (-) 1	Cancer cell line	Male
CVCL_SV17	HAP1 KXD1 (-) 2	Cancer cell line	Male

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.