XG

protein-coding

Xg glycoprotein (Xg blood group), the group of Pseudoautosomal region 1|Blood group antigens

Gene summary

This gene encodes the XG blood group antigen, and is located at the pseudoautosomal boundary on the short (p) arm of chromosome X. The three 5' exons reside in the pseudoautosomal region and the remaining exons within the X-specific end. A truncated copy of this gene is found on the Y chromosome at the pseudoautosomal boundary. It is transcribed, but not expected to make a Y-chromosome specific gene product. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Nov 2008]

Previous symbols:

PBDX

MANE transcript

NM_001141919.2

Inheritance

ClinVar variants

U:29B:1

Top phenotype

XG blood group

gnomAD constraint

pLI —, LoF o/e 1.05

Max pathogenic AF

—

Genomic locus

chrX:2,752,040-2,816,500

External References & Databases

Ensembl (ENSG00000124343)

Transcript & Mutation Effects

hg38 • Region Span ~64.5 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

Clinical Genomic Database (CGD)

XG blood groupBG

Manifestation: Hematologic

Intervention: Hematologic

Rationale: Variants associated with a blood group may be important in specific situations (eg, related to transfusion)

Refs: 7533029; 22356523

Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to XG variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 23

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001141919.2. 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			1 clinvar		1 clinvar	2
missense			26 clinvar			26
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	29	0	1	30

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 34 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001141919.2	RefSeq	NP_001135391.1	11	MANE Select
ENST00000644266.2	Ensembl	ENSP00000494087.1	11	MANE Select
NM_001141920.2	RefSeq	NP_001135392.1	10	Standard
NM_175569.3	RefSeq	NP_780778.1	10	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

biological_process

Molecular Function

molecular_function

Cellular Component

integral component of plasma membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000419513
Coding exons: 11
Length: 64449
Individuals with no LoFs: 125721
Homozygous LoFs: 1
Heterozygous LoFs: 26
Defined: 125748
p: 0.000107

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.0323	90	89.1	1.01	0.00000707	1260
Missense (PolyPhen)		27	25.193	1.0717		335
Synonymous	-0.289	38	35.8	1.06	0.00000329	357
Loss of Function	-0.150	12	11.5	1.05	7.06e-7	180

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00021	0.00018	rare
Latino/Admixed American	0.00027	0.00026	rare
Ashkenazi Jewish	0.000099	0.000099	rare
East Asian	0	0.0	absent
Finnish	0.000062	0.000046	rare
European (Non-Finnish)	0.00012	0.000097	rare
South Asian	0.000095	0.000065	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.659

Intolerance Scores

LoFtool: 0.914
RVIS EVS: 0.42
RVIS percentile EVS: 76.81

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.730

Gene Damage Prediction

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