XKR5

Summary

XKR5 (XK related 5, HGNC:20782) is a protein-coding gene on chromosome 8p23.1, encoding XK-related protein 5 (Q6UX68).

Predicted to be active in plasma membrane.

Source: NCBI Gene 389610 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 104 total
• MANE Select transcript: NM_207411

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:20782
Approved symbol	XKR5
Name	XK related 5
Location	8p23.1
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000275591
Ensembl biotype	protein_coding
Entrez	389610

Gene structure

Transcript identifiers

Ensembl transcripts: 5 — 4 protein_coding, 1 nonsense_mediated_decay

ENST00000618742, ENST00000618990, ENST00000934342, ENST00000934343, ENST00000934344

RefSeq mRNA: 2 — MANE Select: NM_207411 NM_001289973, NM_207411

CCDS: CCDS47763

Canonical transcript exons

ENST00000618742 — 7 exons

Exon	Start	End
ENSE00003725610	6821869	6822038
ENSE00003732305	6823521	6823730
ENSE00003738871	6808517	6812339
ENSE00003739770	6835436	6835524
ENSE00003745663	6815807	6815918
ENSE00003751603	6825165	6825349
ENSE00003758480	6832717	6832900

Expression profiles

Bgee: expression breadth broad, 25 present calls, max score 64.76.

FANTOM5 (CAGE): breadth broad, TPM avg 0.7387 / max 24.5424, expressed in 278 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
91712	0.7387	278

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
stromal cell of endometrium	CL:0002255	64.76	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	60.80	gold quality
ventricular zone	UBERON:0003053	56.89	gold quality
ganglionic eminence	UBERON:0004023	55.24	gold quality
endometrium	UBERON:0001295	55.21	gold quality
smooth muscle tissue	UBERON:0001135	52.68	gold quality
endocervix	UBERON:0000458	50.10	gold quality
myometrium	UBERON:0001296	48.05	gold quality
uterine cervix	UBERON:0000002	47.61	gold quality
bone marrow	UBERON:0002371	47.55	gold quality
sural nerve	UBERON:0015488	46.96	gold quality
placenta	UBERON:0001987	46.05	gold quality
body of uterus	UBERON:0009853	45.09	gold quality
prostate gland	UBERON:0002367	44.45	gold quality
gall bladder	UBERON:0002110	43.76	silver quality
bone marrow cell	CL:0002092	43.35	gold quality
ectocervix	UBERON:0012249	43.10	gold quality
fallopian tube	UBERON:0003889	42.32	gold quality
colonic epithelium	UBERON:0000397	41.24	gold quality
cortex of kidney	UBERON:0001225	40.76	gold quality
muscle tissue	UBERON:0002385	40.75	gold quality
lymph node	UBERON:0000029	39.21	gold quality
right ovary	UBERON:0002118	38.82	silver quality
metanephros cortex	UBERON:0010533	38.20	gold quality
kidney	UBERON:0002113	38.19	silver quality
vermiform appendix	UBERON:0001154	37.71	gold quality
lower esophagus mucosa	UBERON:0035834	37.33	gold quality
prefrontal cortex	UBERON:0000451	36.98	gold quality
leukocyte	CL:0000738	36.97	gold quality
duodenum	UBERON:0002114	36.96	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-ANND-3	no	0.82

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

79 targeting XKR5, 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-3646	100.00	73.56	5283
HSA-MIR-3924	100.00	72.09	2394
HSA-MIR-5193	100.00	67.26	1744
HSA-MIR-4476	100.00	68.18	2030
HSA-MIR-6876-5P	100.00	67.68	2126
HSA-MIR-4534	99.99	66.58	1907
HSA-MIR-4803	99.98	71.99	3117
HSA-MIR-3688-3P	99.97	72.02	2834
HSA-MIR-4487	99.96	64.58	1252
HSA-MIR-545-3P	99.95	70.74	2783
HSA-MIR-6845-3P	99.94	66.88	1439
HSA-MIR-6809-3P	99.91	71.45	3814
HSA-MIR-153-5P	99.89	73.86	6317
HSA-MIR-765	99.84	68.24	2442
HSA-MIR-577	99.78	69.13	2479
HSA-MIR-11181-3P	99.75	66.38	2205
HSA-MIR-4306	99.72	70.50	3630
HSA-MIR-1283	99.69	72.42	3009
HSA-MIR-4663	99.62	65.33	957
HSA-MIR-1260A	99.61	66.67	1098
HSA-MIR-1260B	99.61	66.67	1098
HSA-MIR-516B-5P	99.56	66.33	1495
HSA-MIR-1252-3P	99.55	67.71	2862
HSA-MIR-671-5P	99.52	67.11	1277
HSA-MIR-4325	99.49	72.20	1342
HSA-MIR-4441	99.49	66.56	3216
HSA-MIR-766-5P	99.47	67.91	2225
HSA-MIR-582-5P	99.47	70.79	2635
HSA-MIR-3612	99.45	66.02	1333
HSA-MIR-650	99.45	65.77	1309

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	xkr5b	ENSDARG00000097530
danio_rerio	xkr5a	ENSDARG00000103017
mus_musculus	Xkr5	ENSMUSG00000039814
rattus_norvegicus	Xkr5	ENSRNOG00000028636

Paralogs (5): XKR8 (ENSG00000158156), XKR6 (ENSG00000171044), XKR4 (ENSG00000206579), XKR9 (ENSG00000221947), XKR7 (ENSG00000260903)

Protein

Protein identifiers

XK-related protein 5 — Q6UX68 (reviewed: Q6UX68)

All UniProt accessions (1): Q6UX68

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Cell membrane.

Miscellaneous. May be produced at very low levels due to a premature stop codon in the mRNA, leading to nonsense-mediated mRNA decay.

Similarity. Belongs to the XK family.

Isoforms (2)

UniProt ID	Names	Canonical?
Q6UX68-1	1, 5a	yes
Q6UX68-3	2

RefSeq proteins (2): NP_001276902, NP_997294* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR018629	XK-rel	Family
IPR050895	XK-related_scramblase	Family

Pfam: PF09815

UniProt features (17 total): transmembrane region 5, compositionally biased region 5, region of interest 3, splice variant 2, chain 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q6UX68-F1	62.30	0.30

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 31 (showing top): MIKKELSEN_NPC_HCP_WITH_H3K4ME3_AND_H3K27ME3, GSE13522_WT_VS_IFNAR_KO_SKING_T_CRUZI_Y_STRAIN_INF_DN, MIR4306, MIR4644, MIR185_5P, MIR942_5P, MIR6739_3P, MIR7154_3P, EWSR1_TARGET_GENES, NOTCH3_TARGET_GENES, GSE20366_TREG_VS_NAIVE_CD4_TCELL_HOMEOSTATIC_CONVERSION_UP, GSE2197_CPG_DNA_VS_UNTREATED_IN_DC_DN, HE_LIM_SUN_FETAL_LUNG_C7_PROLIFERATING_SCHWANN_CELL, GSE2770_IL12_VS_IL4_TREATED_ACT_CD4_TCELL_48H_UP, GSE4142_NAIVE_VS_GC_BCELL_DN

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (2): plasma membrane (GO:0005886), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
membrane	1
cell periphery	1
cellular anatomical structure	1

Protein interactions and networks

STRING

196 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
XKR5	SRRM5	B3KS81	599
XKR5	CCDC70	Q6NSX1	507
XKR5	VWA5B1	Q5TIE3	507
XKR5	USP17L1	Q7RTZ2	447
XKR5	TATDN2	Q93075	437
XKR5	PRSS45P	Q7RTY3	434
XKR5	SYNE3	Q6ZMZ3	417
XKR5	DUSP21	Q9H596	411
XKR5	ZBTB47	Q9UFB7	396
XKR5	SDR42E1	Q8WUS8	374
XKR5	ZNF823	P16415	374
XKR5	ZFP3	Q96NJ6	370
XKR5	DEFB107A	Q8IZN7	369
XKR5	CYB5D2	Q8WUJ1	368
XKR5	KEL	P23276	356

IntAct

2 interactions, top by confidence:

A	B	Type	Score
XKR5	VIM	psi-mi:“MI:0915”(physical association)	0.400

BioGRID (1): XKR5 (Proximity Label-MS)

ESM2 similar proteins: A0JN53, A0PJX8, A1L1L2, A1L3T7, A4FV45, B0BMG8, E2JF22, G3HQ82, O15360, O43299, O70491, P60330, Q0KL00, Q0V8E7, Q17Q97, Q24JP3, Q3U829, Q49LS3, Q4QR83, Q562E7, Q5ND34, Q5R7B4, Q5T1A1, Q5XG04, Q6NUQ4, Q6PH58, Q6UX68, Q7L4E1, Q7Z412, Q8BGI5, Q8BM55, Q8BSD4, Q8BXV2, Q8C3R1, Q8C7B8, Q8IXR5, Q8K0R6, Q8N6S5, Q8R115, Q8VCA6

Diamond homologs: E9Q6C8, Q49LS1, Q49LS3, Q49LS4, Q49LS7, Q49LS8, Q49LS9, Q5GH56, Q5GH57, Q5GH59, Q5GH62, Q5GH64, Q5GH66, Q5GH67, Q5GH72, Q5GH73, Q5GH76, Q6UX68, Q8C0T0, Q9H6D3, Q49LS6, Q49LR9, Q49LS0, Q4VV71, Q5GH70

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	94
Likely benign	3
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1115 predictions. Top by Δscore:

Variant	Effect	Δscore
8:6815806:CCAAT:C	donor_gain	1.0000
8:6815929:C:CT	acceptor_gain	1.0000
8:6815929:C:T	acceptor_gain	1.0000
8:6821886:T:TA	donor_gain	1.0000
8:6825161:TCACC:T	donor_loss	1.0000
8:6825162:CACCT:C	donor_loss	1.0000
8:6825163:ACC:A	donor_loss	1.0000
8:6825164:C:G	donor_loss	1.0000
8:6825164:CCTGG:C	donor_gain	1.0000
8:6815800:GACTT:G	donor_loss	0.9900
8:6815801:ACTT:A	donor_loss	0.9900
8:6815802:CTT:C	donor_loss	0.9900
8:6815803:TTA:T	donor_loss	0.9900
8:6815804:T:TG	donor_loss	0.9900
8:6815805:A:AC	donor_gain	0.9900
8:6815805:ACCAA:A	donor_loss	0.9900
8:6815806:C:CC	donor_gain	0.9900
8:6815806:C:G	donor_loss	0.9900
8:6815930:A:T	acceptor_gain	0.9900
8:6821880:TG:T	donor_gain	0.9900
8:6822039:C:CC	acceptor_gain	0.9900
8:6825163:A:AC	donor_gain	0.9900
8:6825164:C:CC	donor_gain	0.9900
8:6825347:TGCCT:T	acceptor_loss	0.9900
8:6825350:C:CA	acceptor_loss	0.9900
8:6825350:C:CC	acceptor_gain	0.9900
8:6825351:T:A	acceptor_loss	0.9900
8:6835435:CG:C	donor_gain	0.9900
8:6835435:CGCG:C	donor_gain	0.9900
8:6815917:ACCTG:A	acceptor_loss	0.9800

AlphaMissense

4425 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
8:6832800:G:C	S53R	0.965
8:6832800:G:T	S53R	0.965
8:6832802:T:G	S53R	0.965
8:6823570:A:C	S196R	0.961
8:6823570:A:T	S196R	0.961
8:6823572:T:G	S196R	0.961
8:6822030:A:G	W216R	0.955
8:6822030:A:T	W216R	0.955
8:6821875:G:C	F267L	0.954
8:6821875:G:T	F267L	0.954
8:6821877:A:G	F267L	0.954
8:6815905:T:A	E274V	0.941
8:6821956:G:C	F240L	0.936
8:6821956:G:T	F240L	0.936
8:6821958:A:G	F240L	0.936
8:6822012:A:G	W222R	0.929
8:6822012:A:T	W222R	0.929
8:6822013:G:C	F221L	0.924
8:6822013:G:T	F221L	0.924
8:6822015:A:G	F221L	0.924
8:6812021:T:A	K413I	0.923
8:6812020:T:A	K413N	0.922
8:6812020:T:G	K413N	0.922
8:6823558:G:C	F200L	0.922
8:6823558:G:T	F200L	0.922
8:6823560:A:G	F200L	0.922
8:6821943:C:G	G245R	0.920
8:6821943:C:T	G245R	0.920
8:6823710:A:G	W150R	0.920
8:6823710:A:T	W150R	0.920

dbSNP variants (sampled 300 via entrez): RS1000007943 (8:6833093 G>A,C), RS1000151796 (8:6812166 G>A,C), RS1000179128 (8:6808839 C>A,T), RS1000201861 (8:6833828 C>G), RS1000254231 (8:6833647 C>T), RS1000323429 (8:6831534 G>C), RS1000448715 (8:6834687 G>A), RS1000449000 (8:6812947 G>C), RS1000467290 (8:6810541 G>A,C), RS1000472557 (8:6820542 T>G), RS1000479917 (8:6834770 T>C), RS1000500559 (8:6830366 C>A,G), RS1000585843 (8:6816507 C>T), RS1000654239 (8:6831348 G>A), RS1000667709 (8:6824560 T>A,C)

Disease associations

OMIM: gene `` | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

1 associations (top):

Study	Trait	p-value
GCST90002399_190	Neutrophil percentage of white cells	4.000000e-09

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0007990	neutrophil percentage of leukocytes

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

12 total (human), top 12 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
perfluorooctanoic acid	affects cotreatment, decreases expression, increases expression	2
aflatoxin B2	increases methylation	1
perfluorooctane sulfonic acid	affects cotreatment, decreases expression	1
perfluoro-n-nonanoic acid	increases expression	1
perfluorohexanesulfonic acid	affects cotreatment, decreases expression	1
Sunitinib	decreases expression	1
Benzo(a)pyrene	increases methylation	1
Calcitriol	affects cotreatment, increases expression	1
Phthalic Acids	increases methylation	1
Testosterone	affects cotreatment, increases expression	1
Aflatoxin B1	decreases methylation	1
Okadaic Acid	decreases expression	1

Clinical trials (associated diseases)

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