XG

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

Basic information

Region (hg38): X:2752039-2816500

Previous symbols: [ "PBDX" ]

Links

ENSG00000124343 ∙ NCBI:7499 ∙ OMIM:300879 ∙ HGNC:12806 ∙ Uniprot:P55808 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
XG blood group	BG	Hematologic	Variants associated with a blood group may be important in specific situations (eg, related to transfusion)	Hematologic	7533029; 22356523

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the XG gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the XG gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous					1	1
missense			8			8
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	8	0	1

Variants in XG

This is a list of pathogenic ClinVar variants found in the XG region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
X-2782081-C-T		not specified	Uncertain significance (Aug 17, 2022)
X-2782104-C-G		not specified	Uncertain significance (Jun 22, 2021)
X-2789673-C-G		not specified	Uncertain significance (Dec 13, 2022)
X-2789703-G-A		not specified	Uncertain significance (Feb 10, 2023)
X-2794595-C-T		not specified	Uncertain significance (Jun 10, 2022)
X-2797355-C-A		not specified	Uncertain significance (Apr 12, 2024)
X-2806704-G-T		not specified	Uncertain significance (Jan 22, 2024)
X-2808207-T-C			Benign (Jun 08, 2018)
X-2811333-C-T			Benign (May 19, 2018)
X-2811338-A-C		not specified	Uncertain significance (Jun 07, 2024)
X-2811341-A-G		not specified	Uncertain significance (Oct 17, 2023)
X-2814366-C-T		not specified	Uncertain significance (Feb 22, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
XG	protein_coding	protein_coding	ENST00000419513	11	64449

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
9.69e-9	0.0939	125721	1	26	125748	0.000107

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0323	90	89.1	1.01	0.00000707	1260
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000481	0.000452
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.00	0.00
Finnish	0.0000625	0.0000462
European (Non-Finnish)	0.000123	0.0000967
Middle Eastern	0.00	0.00
South Asian	0.0000946	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.659

Intolerance Scores

• loftool: 0.914
• rvis_EVS: 0.42
• rvis_percentile_EVS: 76.81

Haploinsufficiency Scores

• pHI: 0.152
• hipred: N
• hipred_score: 0.123
• ghis: 0.427

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.730

Gene Damage Prediction

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

Gene ontology

• Biological process: biological_process
• Cellular component: integral component of plasma membrane
• Molecular function: molecular_function