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XKR6

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Summary

XKR6 (XK related 6, HGNC:27806) is a protein-coding gene on chromosome 8p23.1, encoding XK-related protein 6 (Q5GH73).

Predicted to be involved in apoptotic process involved in development; engulfment of apoptotic cell; and phosphatidylserine exposure on apoptotic cell surface. Predicted to be located in membrane. Predicted to be active in plasma membrane.

Source: NCBI Gene 286046 — RefSeq curated summary.

At a glance

  • GWAS associations: 133
  • Clinical variants (ClinVar): 69 total
  • MANE Select transcript: NM_173683

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:27806
Approved symbolXKR6
NameXK related 6
Location8p23.1
Locus typegene with protein product
StatusApproved
Ensembl geneENSG00000171044
Ensembl biotypeprotein_coding
Entrez286046

Gene structure

Transcript identifiers

Ensembl transcripts: 4 — 3 protein_coding, 1 nonsense_mediated_decay

ENST00000297303, ENST00000382461, ENST00000416569, ENST00000529336

RefSeq mRNA: 1 — MANE Select: NM_173683 NM_173683

CCDS: CCDS5978

Canonical transcript exons

ENST00000416569 — 3 exons

ExonStartEnd
ENSE000016704621089604510898916
ENSE000021705461120057611201833
ENSE000040139221092463410924830

Expression profiles

Bgee: expression breadth ubiquitous, 167 present calls, max score 93.57.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 3.3006 / max 73.4476, expressed in 1052 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter IDTPM avgSamples expressed
918241.8789752
918231.0410554
918250.192878
918220.187984

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
buccal mucosa cellCL:000233693.57gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099186.55gold quality
middle temporal gyrusUBERON:000277183.86gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047382.22gold quality
Brodmann (1909) area 23UBERON:001355480.95gold quality
lower esophagus mucosaUBERON:003583478.31gold quality
right testisUBERON:000453478.14gold quality
left testisUBERON:000453377.76gold quality
body of pancreasUBERON:000115077.23gold quality
primary visual cortexUBERON:000243676.81gold quality
granulocyteCL:000009476.57gold quality
mucosa of transverse colonUBERON:000499176.03gold quality
ventricular zoneUBERON:000305375.91gold quality
pancreasUBERON:000126475.90gold quality
islet of LangerhansUBERON:000000675.42gold quality
testisUBERON:000047375.27gold quality
stromal cell of endometriumCL:000225573.88gold quality
spleenUBERON:000210673.59gold quality
esophagus mucosaUBERON:000246973.13gold quality
lymph nodeUBERON:000002973.04gold quality
bone marrow cellCL:000209273.02gold quality
adrenal tissueUBERON:001830372.74gold quality
occipital lobeUBERON:000202172.50gold quality
right lungUBERON:000216772.36gold quality
small intestine Peyer’s patchUBERON:000345472.00gold quality
minor salivary glandUBERON:000183071.90gold quality
body of stomachUBERON:000116171.86gold quality
left adrenal glandUBERON:000123471.74gold quality
skin of abdomenUBERON:000141671.69gold quality
left adrenal gland cortexUBERON:003582571.10gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3no2.36

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

164 targeting XKR6, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-5011-5P100.0083.465820
HSA-MIR-190A-3P100.0080.355520
HSA-MIR-8485100.0077.574731
HSA-MIR-29A-3P100.0073.111835
HSA-MIR-29B-3P100.0073.181833
HSA-MIR-29C-3P100.0073.151833
HSA-MIR-4682100.0068.891258
HSA-MIR-200B-3P100.0073.312693
HSA-MIR-200C-3P100.0073.352685
HSA-MIR-429100.0073.442698
HSA-MIR-3924100.0072.092394
HSA-MIR-3646100.0073.565283
HSA-MIR-511-3P99.9968.851467
HSA-MIR-366299.9973.825684
HSA-MIR-6870-5P99.9968.552115
HSA-MIR-806899.9873.852376
HSA-MIR-569699.9872.364487
HSA-MIR-477599.9875.006394
HSA-MIR-3617-3P99.9867.86918
HSA-MIR-56899.9869.862084
HSA-MIR-4723-5P99.9768.702034
HSA-MIR-569899.9768.492029
HSA-MIR-7111-5P99.9768.482062
HSA-MIR-391099.9571.132227
HSA-MIR-9983-3P99.9471.483631
HSA-MIR-101-3P99.9475.032230
HSA-MIR-6835-3P99.9370.492904
HSA-MIR-539-5P99.9370.302855
HSA-MIR-515-5P99.9269.822343
HSA-MIR-519E-5P99.9269.622358

Literature-anchored findings (GeneRIF, showing 3)

  • XKR6 single nucleotide polymorphism rs7460469 is associated with childhood-onset systemic lupus erythematosus. (PMID:29967481)
  • XKR6 rs7819412 A allele was related to increased serum triglyceride levels in coronary artery disease, total cholesterol levels in ischemic stroke patients and high risk of CAD and ischemic stroke. (PMID:31429711)
  • XKR6 rs7014968 SNP Increases Serum Total Cholesterol Levels and the Risk of Coronary Heart Disease and Ischemic Stroke. (PMID:32024373)

Cross-species orthologs

4 orthologs

OrganismSymbolGene ID
danio_rerioxkr6aENSDARG00000020443
danio_rerioxkr6bENSDARG00000043410
mus_musculusXkr6ENSMUSG00000035067
rattus_norvegicusXkr6ENSRNOG00000011634

Paralogs (5): XKR8 (ENSG00000158156), XKR4 (ENSG00000206579), XKR9 (ENSG00000221947), XKR7 (ENSG00000260903), XKR5 (ENSG00000275591)

Protein

Protein identifiers

XK-related protein 6 — Q5GH73 (reviewed: Q5GH73)

All UniProt accessions (4): Q5GH73, H0YEU9, H7BYF9, Q96KT3

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Cell membrane.

Similarity. Belongs to the XK family.

Isoforms (2)

UniProt IDNamesCanonical?
Q5GH73-11yes
Q5GH73-22

RefSeq proteins (1): NP_775954* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR018629XK-relFamily
IPR050895XK-related_scramblaseFamily

Pfam: PF09815

UniProt features (13 total): transmembrane region 7, compositionally biased region 2, region of interest 2, chain 1, splice variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q5GH73-F164.850.26

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 127 (showing top): TGGTGCT_MIR29A_MIR29B_MIR29C, GOBP_PLASMA_MEMBRANE_ORGANIZATION, GOBP_APOPTOTIC_CELL_CLEARANCE, GOBP_VESICLE_MEDIATED_TRANSPORT, GOBP_REGULATION_OF_MEMBRANE_LIPID_DISTRIBUTION, GOBP_ORGANOPHOSPHATE_ESTER_TRANSPORT, CATTTCA_MIR203, GOBP_ENDOMEMBRANE_SYSTEM_ORGANIZATION, GOBP_APOPTOTIC_PROCESS_INVOLVED_IN_DEVELOPMENT, GOBP_PHOSPHOLIPID_TRANSPORT, GOBP_MEMBRANE_ORGANIZATION, GOBP_MEMBRANE_INVAGINATION, GOBP_IMPORT_INTO_CELL, GOBP_LIPID_LOCALIZATION, TGCCTTA_MIR124A

GO Biological Process (3): engulfment of apoptotic cell (GO:0043652), phosphatidylserine exposure on apoptotic cell surface (GO:0070782), apoptotic process involved in development (GO:1902742)

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:

CategoryTerms
phagocytosis, engulfment1
apoptotic cell clearance1
plasma membrane phospholipid scrambling1
phospholipid scramblase activity1
execution phase of apoptosis1
apoptotic process1
anatomical structure development1
membrane1
cell periphery1
cellular anatomical structure1

Protein interactions and networks

STRING

620 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
XKR6FAM167AQ96KS9743
XKR6MTMR9Q96QG7649
XKR6BLKP51451626
XKR6SLC35G5Q96KT7572
XKR6LCA5LO95447539
XKR6CCM2Q9BSQ5528
XKR6KELP23276505
XKR6PPP1R3BQ86XI6498
XKR6TNKSO95271495
XKR6MSRAQ9UJ68479
XKR6TMEM63BQ5T3F8478
XKR6CTSBP07858477
XKR6PXKQ7Z7A4470
XKR6MFHAS1Q9Y4C4446
XKR6SH3BGRP55822432

IntAct

3 interactions, top by confidence:

ABTypeScore
XKR6VIMpsi-mi:“MI:0915”(physical association)0.400
XKR6SLC27A3psi-mi:“MI:0914”(association)0.350

BioGRID (8): XKR6 (Proximity Label-MS), UBAC2 (Affinity Capture-MS), SLC27A3 (Affinity Capture-MS), THEM6 (Affinity Capture-MS), RETSAT (Affinity Capture-MS), XKR6 (Cross-Linking-MS (XL-MS)), XKR6 (Affinity Capture-RNA), XKR6 (Affinity Capture-RNA)

ESM2 similar proteins: A0JPH4, A2AWP8, A2RRU4, A2SXS5, A4D2P6, A6QM06, D4A6L0, E1BBQ2, E9Q6C8, F1LQY6, O00255, O88559, O94827, P29590, P56726, P97260, P97698, Q0GA42, Q0P5I0, Q0VF94, Q12770, Q17RQ9, Q29RM4, Q49LS8, Q5GH57, Q5GH73, Q5MNU5, Q5SNT2, Q5T848, Q69Z89, Q6DVA0, Q6GQT6, Q6IEE7, Q70EL4, Q8BUM9, Q8C190, Q8C419, Q8NC56, Q8TCT7, Q91ZP9

Diamond homologs: E9Q6C8, Q49LS1, Q49LS4, Q49LS6, Q49LS7, Q49LS8, Q49LS9, Q4VV71, Q5GH56, Q5GH57, Q5GH59, Q5GH64, Q5GH67, Q5GH72, Q5GH73, Q5GH76, Q49LS3, Q5GH62, Q5GH66, Q6UX68, Q8C0T0, Q9H6D3, A8Y2U2, O17386, Q49LR9, Q49LS0, Q5GH70, Q9QXY7

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance64
Likely benign3
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

4033 predictions. Top by Δscore:

VariantEffectΔscore
8:10924632:A:ACdonor_gain1.0000
8:10924633:C:CCdonor_gain1.0000
8:10924633:CAGGG:Cdonor_gain1.0000
8:10924626:GCACT:Gdonor_loss0.9900
8:10924627:CACT:Cdonor_loss0.9900
8:10924628:ACTC:Adonor_loss0.9900
8:10924629:CTCA:Cdonor_loss0.9900
8:10924630:T:TAdonor_loss0.9900
8:10924631:C:CCdonor_loss0.9900
8:10924632:ACAGG:Adonor_loss0.9900
8:10924633:C:CTdonor_loss0.9900
8:10924826:TATAC:Tacceptor_gain0.9900
8:10924827:ATAC:Aacceptor_gain0.9900
8:10924828:TAC:Tacceptor_gain0.9900
8:10924831:C:CAacceptor_loss0.9900
8:10924836:C:CTacceptor_gain0.9900
8:10924836:C:Tacceptor_gain0.9900
8:10924843:A:ACacceptor_gain0.9900
8:10924843:A:Cacceptor_gain0.9900
8:11001950:T:TAdonor_gain0.9900
8:11027729:T:Cacceptor_gain0.9900
8:11104453:G:Cdonor_gain0.9900
8:11137539:CCCA:Cdonor_gain0.9900
8:11200573:TA:Tdonor_loss0.9900
8:10924625:GGCAC:Gdonor_loss0.9800
8:10924633:CA:Cdonor_gain0.9800
8:10924633:CAGG:Cdonor_gain0.9800
8:10924829:AC:Aacceptor_gain0.9800
8:10924830:CC:Cacceptor_gain0.9800
8:10924831:C:CCacceptor_gain0.9800

AlphaMissense

4139 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
8:10898067:C:AR604M1.000
8:10898087:C:AW597C1.000
8:10898087:C:GW597C1.000
8:10898089:A:GW597R1.000
8:10898089:A:TW597R1.000
8:10898124:A:GI585T1.000
8:10898124:A:TI585N1.000
8:11200576:C:AR255M1.000
8:11200793:A:GW183R1.000
8:11200793:A:TW183R1.000
8:10898040:A:GL613P0.999
8:10898057:T:AR607S0.999
8:10898057:T:GR607S0.999
8:10898058:C:AR607I0.999
8:10898058:C:GR607T0.999
8:10898061:A:GL606P0.999
8:10898066:C:AR604S0.999
8:10898066:C:GR604S0.999
8:10898067:C:GR604T0.999
8:10898070:T:AD603V0.999
8:10898070:T:GD603A0.999
8:10898071:C:GD603H0.999
8:10898118:A:CI587S0.999
8:10898124:A:CI585S0.999
8:10898189:G:CF563L0.999
8:10898189:G:TF563L0.999
8:10898190:A:GF563S0.999
8:10898191:A:GF563L0.999
8:10898610:C:TG423E0.999
8:10898611:C:AG423W0.999

dbSNP variants (sampled 300 via entrez): RS1000005280 (8:11021239 G>A), RS1000009708 (8:10964509 T>C), RS1000019071 (8:11108952 C>A,G,T), RS1000020513 (8:10975197 A>G), RS1000024177 (8:11112665 G>A), RS1000032789 (8:11141714 T>C), RS1000034989 (8:10917673 G>A), RS1000042008 (8:11139812 G>A), RS1000045759 (8:11036250 G>C), RS1000050972 (8:11091496 A>C), RS1000051855 (8:11116600 A>C,G), RS1000052895 (8:10905908 C>T), RS1000054024 (8:11193031 T>C), RS1000057864 (8:10945038 G>A), RS1000067437 (8:11053568 T>G)

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

133 associations (top):

StudyTraitp-value
GCST000286_1Triglycerides3.000000e-08
GCST000758_12Triglycerides1.000000e-08
GCST000847_5Retinal vascular caliber4.000000e-07
GCST002322_14Asthma and hay fever4.000000e-07
GCST002527_6Eosinophilic esophagitis5.000000e-08
GCST002928_12Nickel levels1.000000e-06
GCST003103_2Systemic lupus erythematosus8.000000e-06
GCST003998_11Joint mobility (Beighton score)3.000000e-09
GCST004017_1Neuroticism3.000000e-24
GCST004351_19Bone ultrasound measurement (broadband ultrasound attenuation)4.000000e-07
GCST005576_17Intracranial aneurysm7.000000e-07
GCST005752_49Systemic lupus erythematosus1.000000e-07
GCST005835_3Remission after SSRI treatment in MDD or neuroticism1.000000e-12
GCST006170_19Systolic blood pressure x alcohol consumption (light vs heavy) interaction (2df test)1.000000e-12
GCST006172_13Mean arterial pressure x alcohol consumption (light vs heavy) interaction (2df test)3.000000e-09
GCST006172_39Mean arterial pressure x alcohol consumption (light vs heavy) interaction (2df test)2.000000e-08
GCST006434_89Systolic blood pressure x alcohol consumption interaction (2df test)1.000000e-20
GCST007293_1Body fat distribution (arm fat ratio)3.000000e-16
GCST007293_108Body fat distribution (arm fat ratio)8.000000e-14
GCST007293_71Body fat distribution (arm fat ratio)5.000000e-07
GCST007294_182Body fat distribution (trunk fat ratio)1.000000e-07
GCST007325_130General risk tolerance (MTAG)6.000000e-11
GCST007325_168General risk tolerance (MTAG)1.000000e-08
GCST007325_197General risk tolerance (MTAG)2.000000e-08
GCST007325_55General risk tolerance (MTAG)3.000000e-29
GCST007327_49Smoking status (ever vs never smokers)1.000000e-08
GCST007329_16Automobile speeding propensity9.000000e-09
GCST007709_180General factor of neuroticism2.000000e-09
GCST007709_184General factor of neuroticism4.000000e-11
GCST007709_186General factor of neuroticism5.000000e-11

EFO canonical traits (22, from GWAS)

EFO IDTrait name
EFO:0004530triglyceride measurement
EFO:0004731eye measurement
EFO:0007905joint hypermobility measurement
EFO:0007660neuroticism measurement
EFO:0004514bone quantitative ultrasound measurement
EFO:0005658response to selective serotonin reuptake inhibitor
EFO:0006335systolic blood pressure
EFO:0006340mean arterial pressure
EFO:0004329alcohol drinking
EFO:0004341body fat distribution
EFO:0008579risk-taking behaviour
EFO:0004318smoking behavior
EFO:0005670smoking initiation
EFO:0008111diet measurement
EFO:0007863illness severity status
EFO:0004346neuroimaging measurement
EFO:0009819comparative body size at age 10, self-reported
EFO:0005665white matter hyperintensity measurement
EFO:0007789BMI-adjusted waist circumference
EFO:0007788BMI-adjusted waist-hip ratio
EFO:0009863anxiety measurement
EFO:0008039BMI-adjusted hip circumference

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

20 total (human), top 20 by PubMed support.

ChemicalActions (top 5)PubMed papers
bisphenol Aaffects methylation, affects cotreatment, increases methylation2
Benzo(a)pyreneaffects methylation, increases expression2
Valproic Acidaffects expression, decreases expression2
Aflatoxin B1increases methylation2
Cadmium Chloridedecreases expression, increases abundance, increases expression2
methylmercuric chloridedecreases expression1
sodium arsenitedecreases expression1
belinostatincreases expression1
abrineincreases expression1
bisphenol Sdecreases methylation1
Sunitinibdecreases expression1
Fulvestrantaffects cotreatment, increases methylation1
Cadmiumdecreases expression, increases abundance1
Estradioldecreases expression, affects cotreatment1
Ethyl Methanesulfonateincreases expression1
Folic Aciddecreases expression1
Formaldehydeincreases expression1
Methyl Methanesulfonateincreases expression1
Smokedecreases expression1
Antirheumatic Agentsincreases expression1

Clinical trials (associated diseases)

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

About this page

Generated deterministically by Sugi Atlas from primary biomedical databases via BioBTree. Every record on this page traces to a primary source.

Generated
Atlas version
v1.1.2
BioBTree
v2.0.2

Sources 74

This page pulls from 74 datasets indexed by BioBTree:

alphafoldalphamissenseantibodybgeebgee_evidencebindingdbbiogrid_interactionbrendabrenda_kineticsccdscellosauruschembl_activitychembl_targetciviccivic_evidenceclingen_dosageclingen_gene_validityclinical_trialsclinvarcollectrictd_gene_interactiondbsnpdepmapdiamond_similarityefoensemblentrezesm2_similarityexonfantom5_genefantom5_promotergenccgenerifgogoparentgtopdbgwasgwas_studyhgnchpointactinterprointogenjasparmeshmimmirdbmondomsigdborphanetorthologparalogpdbpfampharmgkb_clinicalpharmgkb_genepharmgkb_guidelinepharmgkb_variantpubchempubchem_activitypubchem_assaypubmedreactomerefseqrhearnacentralscxa_expressionscxa_gene_experimentsignorspliceaistring_interactiontranscriptufeatureuniprot