XKRX

protein-coding

XK related X-linked, the group of XK related family

Gene summary

This gene encodes a protein that is related to a component of the XK/Kell complex of the Kell blood group system. The encoded protein includes several transmembrane domains, is known to be exposed to the cell surface, and may function as a membrane transporter. [provided by RefSeq, May 2010]

MANE transcript

NM_212559.3

Inheritance

—

ClinVar variants

U:77B:7

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.62

Max pathogenic AF

—

Genomic locus

chrX:100,913,445-100,929,433

External References & Databases

Ensembl (ENSG00000182489)

Transcript & Mutation Effects

hg38 • Region Span ~16.0 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 XKRX variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 50

not providedTotal: 4

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_212559.3. 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			3 clinvar	3 clinvar		6
missense			68 clinvar	4 clinvar		72
nonsense			5 clinvar			5
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	77	7	0	84

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 8 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_212559.3	RefSeq	NP_997724.2	3	MANE Select
ENST00000372956.3	Ensembl	ENSP00000362047.2	3	MANE Select
ENST00000468904.1	Ensembl	ENSP00000419884.1	2	Standard
ENST00001109707.1	Ensembl	ENSP00000779512.1	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Cellular Component

plasma membrane
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000372956
Coding exons: 3
Length: 15992
Individuals with no LoFs: 125733
Homozygous LoFs: 8
Heterozygous LoFs: 4
Defined: 125745
p: 0.0000477

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.482	152	170	0.896	0.0000130	2931
Missense (PolyPhen)		58	73.253	0.79178		1281
Synonymous	0.631	59	65.5	0.901	0.00000464	904
Loss of Function	1.20	7	11.4	0.616	9.24e-7	193

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000036	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00030	0.00022	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000024	0.000018	rare
South Asian	0.00026	0.00016	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.100

Intolerance Scores

LoFtool: 0.561
RVIS EVS: 0.33
RVIS percentile EVS: 73.27

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Indispensability pred.: N
Indispensability score: 0.307

Gene Damage Prediction

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