XKR9

protein-coding

XK related 9, the group of XK related family

Gene summary

Enables phospholipid scramblase activity. Involved in phosphatidylserine exposure on apoptotic cell surface. Predicted to be located in plasma membrane. Predicted to be active in membrane. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_001011720.2

Inheritance

—

ClinVar variants

U:56B:5

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.99

Max pathogenic AF

—

Genomic locus

chr8:70,669,339-70,790,371

External References & Databases

Ensembl (ENSG00000221947)

Transcript & Mutation Effects

hg38 • Region Span ~121.0 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 XKR9 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 55

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001011720.2. 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			2 clinvar			2
missense			53 clinvar	4 clinvar		57
nonsense					1 clinvar	1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	56	4	1	61

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 29 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001011720.2	RefSeq	NP_001011720.1	3	MANE Select
ENST00000408926.8	Ensembl	ENSP00000386141.3	3	MANE Select
NM_001287258.2	RefSeq	NP_001274187.1	2	Standard
NM_001287259.2	RefSeq	NP_001274188.1	3	Standard

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: ENST00000408926
Coding exons: 3
Length: 121007
Individuals with no LoFs: 124244
Homozygous LoFs: 40
Heterozygous LoFs: 1423
Defined: 125707
p: 0.00584

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-1.71	252	186	1.35	0.00000834	2465
Missense (PolyPhen)		59	49.239	1.1982		685
Synonymous	-0.775	73	65.0	1.12	0.00000319	682
Loss of Function	0.0433	13	13.2	0.987	5.52e-7	184

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00081	0.00080	rare
Latino/Admixed American	0.0029	0.0028	notable
Ashkenazi Jewish	0	0.0	absent
East Asian	0.069	0.067	notable
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.00072	0.00071	rare
South Asian	0.0020	0.0018	notable
Other	0.0040	0.0038	notable

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

LoFtool: 0.663
RVIS EVS: 1.24
RVIS percentile EVS: 93.39

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.593

Gene Damage Prediction

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