XKR7

Summary

XKR7 (XK related 7, HGNC:23062) is a protein-coding gene on chromosome 20q11.21, encoding XK-related protein 7 (Q5GH72).

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 343702 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 89 total — 1 likely-pathogenic
• MANE Select transcript: NM_001011718

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:23062
Approved symbol	XKR7
Name	XK related 7
Location	20q11.21
Locus type	gene with protein product
Status	Approved
Aliases	dJ310O13.4
Ensembl gene	ENSG00000260903
Ensembl biotype	protein_coding
Entrez	343702

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000562532

RefSeq mRNA: 1 — MANE Select: NM_001011718 NM_001011718

CCDS: CCDS33459

Canonical transcript exons

ENST00000562532 — 3 exons

Exon	Start	End
ENSE00000661141	31995068	31995270
ENSE00001468792	31968151	31968759
ENSE00002599389	31996505	32003387

Expression profiles

Bgee: expression breadth broad, 54 present calls, max score 85.00.

FANTOM5 (CAGE): breadth broad, TPM avg 2.2683 / max 329.9072, expressed in 304 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
183997	2.2683	304

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
cortical plate	UBERON:0005343	85.00	gold quality
ganglionic eminence	UBERON:0004023	83.91	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	82.88	silver quality
cerebellar hemisphere	UBERON:0002245	81.22	gold quality
cerebellar cortex	UBERON:0002129	81.19	gold quality
right hemisphere of cerebellum	UBERON:0014890	80.92	gold quality
cerebellum	UBERON:0002037	79.98	gold quality
parotid gland	UBERON:0001831	78.85	gold quality
pancreatic ductal cell	CL:0002079	74.10	silver quality
islet of Langerhans	UBERON:0000006	73.57	gold quality
upper arm skin	UBERON:0004263	68.63	gold quality
pituitary gland	UBERON:0000007	66.09	gold quality
cardiac muscle of right atrium	UBERON:0003379	66.04	gold quality
left ventricle myocardium	UBERON:0006566	65.47	gold quality
prefrontal cortex	UBERON:0000451	64.99	gold quality
adenohypophysis	UBERON:0002196	64.41	gold quality
ventricular zone	UBERON:0003053	62.13	gold quality
myocardium	UBERON:0002349	62.04	gold quality
cerebellar vermis	UBERON:0004720	61.92	gold quality
frontal cortex	UBERON:0001870	61.40	gold quality
right frontal lobe	UBERON:0002810	61.10	gold quality
neocortex	UBERON:0001950	61.09	gold quality
ileal mucosa	UBERON:0000331	59.77	silver quality
Brodmann (1909) area 9	UBERON:0013540	59.68	gold quality
anterior cingulate cortex	UBERON:0009835	59.19	gold quality
tibialis anterior	UBERON:0001385	59.01	silver quality
dorsolateral prefrontal cortex	UBERON:0009834	58.85	gold quality
skeletal muscle tissue of biceps brachii	UBERON:0004502	58.76	gold quality
Brodmann (1909) area 46	UBERON:0006483	58.57	gold quality
cerebral cortex	UBERON:0000956	58.01	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	2.12

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

52 targeting XKR7, 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-29A-3P	100.00	73.11	1835
HSA-MIR-29B-3P	100.00	73.18	1833
HSA-MIR-29C-3P	100.00	73.15	1833
HSA-MIR-188-3P	100.00	68.76	1240
HSA-MIR-6508-5P	99.92	70.67	2465
HSA-MIR-5682	99.89	72.56	1005
HSA-MIR-345-3P	99.89	70.23	1421
HSA-MIR-8067	99.86	69.59	2260
HSA-MIR-204-5P	99.79	71.62	2439
HSA-MIR-211-5P	99.79	71.65	2440
HSA-MIR-3156-3P	99.76	66.72	939
HSA-MIR-6887-3P	99.66	67.83	1778
HSA-MIR-1260A	99.61	66.67	1098
HSA-MIR-1260B	99.61	66.67	1098
HSA-MIR-5003-5P	99.61	69.13	1624
HSA-MIR-6832-3P	99.52	70.44	1726
HSA-MIR-6871-3P	99.43	68.85	741
HSA-MIR-3960	99.41	66.11	96
HSA-MIR-584-3P	99.35	67.69	1082
HSA-MIR-3692-5P	99.29	67.04	1421
HSA-MIR-3191-5P	99.24	66.52	1722
HSA-MIR-544B	99.18	67.41	1632
HSA-MIR-6071	99.16	67.77	1780
HSA-MIR-4478	99.07	65.16	2320
HSA-MIR-320A-5P	98.88	66.75	1248
HSA-MIR-4686	98.77	66.87	964
HSA-MIR-6780A-3P	98.42	67.49	1518
HSA-MIR-5088-3P	98.29	66.63	1310
HSA-MIR-8072	98.27	66.24	83
HSA-MIR-93-3P	98.15	66.65	1309

Cross-species orthologs

1 orthologs

Organism	Symbol	Gene ID
mus_musculus	Xkr7	ENSMUSG00000042631

Paralogs (5): XKR8 (ENSG00000158156), XKR6 (ENSG00000171044), XKR4 (ENSG00000206579), XKR9 (ENSG00000221947), XKR5 (ENSG00000275591)

Protein

Protein identifiers

XK-related protein 7 — Q5GH72 (reviewed: Q5GH72)

All UniProt accessions (1): Q5GH72

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Cell membrane.

Similarity. Belongs to the XK family.

RefSeq proteins (1): NP_001011718* (*=MANE)

Domains & families (InterPro)

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

Pfam: PF09815

UniProt features (13 total): transmembrane region 7, region of interest 3, compositionally biased region 2, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q5GH72-F1	69.78	0.35

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 44 (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, GOBP_ENDOMEMBRANE_SYSTEM_ORGANIZATION, GOBP_APOPTOTIC_PROCESS_INVOLVED_IN_DEVELOPMENT, GOBP_PHOSPHOLIPID_TRANSPORT, GOBP_MEMBRANE_ORGANIZATION, GOBP_MEMBRANE_INVAGINATION, chr20q11, GOBP_IMPORT_INTO_CELL, GOBP_LIPID_LOCALIZATION, GOBP_EXECUTION_PHASE_OF_APOPTOSIS

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:

Category	Terms
phagocytosis, engulfment	1
apoptotic cell clearance	1
plasma membrane phospholipid scrambling	1
phospholipid scramblase activity	1
execution phase of apoptosis	1
apoptotic process	1
anatomical structure development	1
membrane	1
cell periphery	1
cellular anatomical structure	1

Protein interactions and networks

STRING

512 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
XKR7	CCM2L	Q9NUG4	589
XKR7	PGBD5	Q8N414	579
XKR7	CCDC137	Q6PK04	530
XKR7	ZC3H3	Q8IXZ2	501
XKR7	ARFGAP3	Q9NP61	454
XKR7	MRPL12	P52815	407
XKR7	KEL	P23276	380
XKR7	F6RGN5	F6RGN5	373
XKR7	SLC25A10	Q9UBX3	372
XKR7	POFUT1	Q9H488	355
XKR7	VEGFD	O43915	341
XKR7	PFKFB1	P16118	331
XKR7	DUSP15	Q9H1R2	326
XKR7	KIF3B	O15066	323
XKR7	ATP2B2	Q01814	315

IntAct

120 interactions, top by confidence:

A	B	Type	Score
	VAPB	psi-mi:“MI:0914”(association)	0.500
XKR7	SNX27	psi-mi:“MI:0407”(direct interaction)	0.440
MAST2	XKR7	psi-mi:“MI:0407”(direct interaction)	0.440
XKR7	PDZD2	psi-mi:“MI:0407”(direct interaction)	0.440
XKR7	SNTG1	psi-mi:“MI:0407”(direct interaction)	0.440
XKR7	DLG1	psi-mi:“MI:0407”(direct interaction)	0.440
SNTB1	XKR7	psi-mi:“MI:0407”(direct interaction)	0.440
XKR7	SYNJ2BP	psi-mi:“MI:0407”(direct interaction)	0.440
XKR7	SNTA1	psi-mi:“MI:0407”(direct interaction)	0.440
XKR7	MAST1	psi-mi:“MI:0407”(direct interaction)	0.440
XKR7	DLG4	psi-mi:“MI:0407”(direct interaction)	0.440
XKR7	MAGI2	psi-mi:“MI:0407”(direct interaction)	0.440
XKR7	PDZD7	psi-mi:“MI:0407”(direct interaction)	0.440
XKR7	PTPN3	psi-mi:“MI:0407”(direct interaction)	0.440
XKR7	DLG3	psi-mi:“MI:0407”(direct interaction)	0.440
XKR7	DLG2	psi-mi:“MI:0407”(direct interaction)	0.440
XKR7	FRMPD2	psi-mi:“MI:0407”(direct interaction)	0.440
SCRIB	XKR7	psi-mi:“MI:0407”(direct interaction)	0.440
XKR7	LIN7C	psi-mi:“MI:0407”(direct interaction)	0.440
XKR7	RADIL	psi-mi:“MI:0407”(direct interaction)	0.440
XKR7	LNX2	psi-mi:“MI:0407”(direct interaction)	0.440
XKR7	SNTG2	psi-mi:“MI:0407”(direct interaction)	0.440
XKR7	HTRA1	psi-mi:“MI:0407”(direct interaction)	0.440
XKR7	RHPN1	psi-mi:“MI:0407”(direct interaction)	0.440
XKR7	PATJ	psi-mi:“MI:0407”(direct interaction)	0.440
XKR7	LNX1	psi-mi:“MI:0407”(direct interaction)	0.440
XKR7	ERBIN	psi-mi:“MI:0407”(direct interaction)	0.440
XKR7	ARHGEF11	psi-mi:“MI:0407”(direct interaction)	0.440

BioGRID (1): XKR7 (Affinity Capture-MS)

ESM2 similar proteins: A0A5F4BST2, A0PJX4, A0RZB4, A1L515, A2A9Q0, A2BDG0, A6QQ85, A6XN32, A9JSM3, B0FP48, D3YZZ2, D4A2Q0, E5RIL1, F1SAM7, P01183, Q1RMK9, Q3UPR0, Q3ZCQ3, Q5BIV7, Q5BIV9, Q5BK01, Q5GH56, Q5GH64, Q5GH72, Q5SNT2, Q5T7M4, Q6IEE6, Q6PRD1, Q6UWJ8, Q70RD5, Q864V4, Q86UD0, Q8BWU1, Q8BX43, Q8CCB5, Q8IVY1, Q8K064, Q8K2Y3, Q8K5A9, Q8N9H8

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, Q49LS0, Q49LR9, Q5GH70, Q9QXY7

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 84 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
Ras activation upon Ca2+ influx through NMDA receptor	5	51.9×	1e-06
Unblocking of NMDA receptors, glutamate binding and activation	5	49.4×	1e-06
Negative regulation of NMDA receptor-mediated neuronal transmission	5	49.4×	1e-06
Assembly and cell surface presentation of NMDA receptors	10	46.1×	9e-13
Dopamine Neurotransmitter Release Cycle	5	45.1×	2e-06
Long-term potentiation	5	43.3×	2e-06
Neurexins and neuroligins	11	39.4×	5e-13
Protein-protein interactions at synapses	7	33.8×	8e-08

GO biological processes:

GO term	Partners	Fold	FDR
establishment or maintenance of epithelial cell apical/basal polarity	10	72.6×	3e-14
protein localization to synapse	6	57.5×	9e-08
receptor clustering	7	54.6×	9e-09
regulation of postsynaptic membrane neurotransmitter receptor levels	7	43.4×	3e-08
protein-containing complex assembly	8	11.4×	4e-05
cell-cell adhesion	8	10.2×	7e-05
regulation of small GTPase mediated signal transduction	5	9.0×	5e-03
chemical synaptic transmission	7	6.8×	2e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	1
Uncertain significance	87
Likely benign	1
Benign	0

Top pathogenic / likely-pathogenic (1)

Variant ID	HGVS	Classification
982222	NM_001011718.2(XKR7):c.1475G>A (p.Arg492His)	Likely pathogenic

SpliceAI

426 predictions. Top by Δscore:

Variant	Effect	Δscore
20:31995062:CCGCA:C	acceptor_loss	1.0000
20:31995266:GCCGG:G	donor_gain	1.0000
20:31995267:CCGGG:C	donor_loss	1.0000
20:31995269:GG:G	donor_gain	1.0000
20:31995269:GGGT:G	donor_loss	1.0000
20:31995270:GG:G	donor_gain	1.0000
20:31995271:G:GG	donor_gain	1.0000
20:31995272:T:A	donor_loss	1.0000
20:31997452:GT:G	donor_gain	1.0000
20:31968758:AG:A	donor_loss	0.9900
20:31968759:GG:G	donor_loss	0.9900
20:31968760:GTAGG:G	donor_loss	0.9900
20:31968761:T:A	donor_loss	0.9900
20:31995066:A:AG	acceptor_gain	0.9900
20:31995066:AG:A	acceptor_gain	0.9900
20:31995067:G:GT	acceptor_gain	0.9900
20:31995067:GG:G	acceptor_gain	0.9900
20:31995067:GGT:G	acceptor_gain	0.9900
20:31995067:GGTAC:G	acceptor_gain	0.9900
20:31996503:A:AG	acceptor_gain	0.9900
20:31996504:G:GG	acceptor_gain	0.9900
20:31997370:G:GT	donor_gain	0.9900
20:31995063:C:A	acceptor_gain	0.9800
20:31995067:GGTA:G	acceptor_gain	0.9800
20:31996499:CCACA:C	acceptor_loss	0.9800
20:31996500:CACA:C	acceptor_loss	0.9800
20:31996501:ACAGC:A	acceptor_loss	0.9800
20:31996503:A:AC	acceptor_loss	0.9800
20:31996504:G:GT	acceptor_loss	0.9800
20:31996504:GCC:G	acceptor_gain	0.9800

AlphaMissense

3691 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
20:31968759:G:T	R195M	0.999
20:31996723:T:A	W336R	0.999
20:31996723:T:C	W336R	0.999
20:31996810:G:C	G365R	0.999
20:31997322:G:C	W535C	0.999
20:31997322:G:T	W535C	0.999
20:31968474:C:G	P100R	0.998
20:31968497:A:C	S108R	0.998
20:31968499:C:A	S108R	0.998
20:31968499:C:G	S108R	0.998
20:31968506:T:A	W111R	0.998
20:31968506:T:C	W111R	0.998
20:31996540:T:A	W275R	0.998
20:31996540:T:C	W275R	0.998
20:31996811:G:A	G365D	0.998
20:31997320:T:A	W535R	0.998
20:31997320:T:C	W535R	0.998
20:31968474:C:A	P100H	0.997
20:31995163:A:T	D227V	0.997
20:31996765:T:C	F350L	0.997
20:31996767:C:A	F350L	0.997
20:31996767:C:G	F350L	0.997
20:31996811:G:T	G365V	0.997
20:31997285:T:C	I523T	0.997
20:31997348:T:C	L544P	0.997
20:31997351:G:C	R545P	0.997
20:31968759:G:C	R195T	0.996
20:31995162:G:T	D227Y	0.996
20:31995208:C:A	P242Q	0.996
20:31995208:C:G	P242R	0.996

dbSNP variants (sampled 300 via entrez): RS1000004304 (20:31998034 G>A,T), RS1000022923 (20:31981918 A>G), RS1000039415 (20:31967064 C>G), RS1000093065 (20:31992527 A>G,T), RS1000192634 (20:32003534 C>T), RS1000209746 (20:31968681 A>C,G), RS1000261060 (20:31995699 A>G), RS1000387950 (20:32001974 C>A), RS1000456780 (20:31981663 G>A,T), RS1000620392 (20:31999801 A>G), RS1000695082 (20:31995493 C>A,T), RS1000712274 (20:32000639 T>C), RS1000744882 (20:32000359 G>A), RS1001106861 (20:31968748 C>A,T), RS1001264032 (20:31981353 G>C)

Disease associations

OMIM: gene `` | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (1): Moyamoya angiopathy (Orphanet:477768)

HPO phenotypes

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

GWAS associations

1 associations (top):

Study	Trait	p-value
GCST90000025_637	Appendicular lean mass	1.000000e-11

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0004980	appendicular lean mass

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

6 total (human), top 6 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
aristolochic acid I	decreases expression	1
benzo(e)pyrene	decreases methylation	1
Benzo(a)pyrene	increases methylation	1
Methapyrilene	decreases methylation	1
Valproic Acid	decreases methylation	1
Aflatoxin B1	decreases methylation	1

Clinical trials (associated diseases)

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