XKR7

protein-coding

XK related 7, the group of XK related family

Gene summary

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. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

C20orf159

MANE transcript

NM_001011718.2

Inheritance

—

ClinVar variants

P:1U:89B:1

Top phenotype

Moyamoya angiopathy

gnomAD constraint

pLI —, LoF o/e 0.12

Max pathogenic AF

—

Genomic locus

chr20:31,968,151-32,003,387

External References & Databases

Ensembl (ENSG00000260903)

Transcript & Mutation Effects

hg38 • Region Span ~35.2 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to XKR7 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 88

not providedTotal: 2

Moyamoya angiopathyTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001011718.2. Only rare variants are included.

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		1 clinvar	87 clinvar	1 clinvar		89
nonsense						0
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	1	89	1	0	91

Highest pathogenic variant AF is 0.000034165438

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 2 of 2 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001011718.2	RefSeq	NP_001011718.1	3	MANE Select
ENST00000562532.3	Ensembl	ENSP00000477059.1	3	MANE Select

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

engulfment of apoptotic cell
phosphatidylserine exposure on apoptotic cell surface
apoptotic process involved in development

Cellular Component

plasma membrane
membrane
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000562532
Coding exons: 3
Length: 35386
Individuals with no LoFs: 125738
Homozygous LoFs: 0
Heterozygous LoFs: 5
Defined: 125743
p: 0.0000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.57	256	337	0.760	0.0000209	3624
Missense (PolyPhen)		108	157.88	0.68407		1699
Synonymous	1.41	128	150	0.854	0.00000912	1279
Loss of Function	3.31	2	16.5	0.121	7.08e-7	192

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	0.000054	0.000054	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000036	0.000035	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

LoFtool: 0.0278
RVIS EVS: -0.36
RVIS percentile EVS: 28.93

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Indispensability pred.: N
Indispensability score: 0.370

Gene Damage Prediction

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