XAB2

XPA binding protein 2, the group of Nucleotide excision repair|Spliceosomal C complex|Spliceosomal B complex|Spliceosomal Bact complex|Spliceosomal P complex

Basic information

Region (hg38): 19:7619525-7629545

Links

ENSG00000076924

∙ NCBI:56949 ∙ OMIM:610850 ∙ HGNC:14089 ∙ Uniprot:Q9HCS7 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the XAB2 gene.

not_specified (116 variants)
not_provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the XAB2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000020196.3. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			116 clinvar			116
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	117	0	0

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
XAB2	protein_coding	protein_coding	ENST00000358368	19	10041

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.973	0.0272	125718	0	30	125748	0.000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.94	471	605	0.779	0.0000450	5537
Missense in Polyphen		127	182.89	0.69439		1539
Synonymous	-1.36	280	252	1.11	0.0000195	1661
Loss of Function	5.43	9	50.8	0.177	0.00000260	520

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000958	0.0000958
Ashkenazi Jewish	0.0000997	0.0000992
East Asian	0.0000546	0.0000544
Finnish	0.000140	0.000139
European (Non-Finnish)	0.0000882	0.0000879
Middle Eastern	0.0000546	0.0000544
South Asian	0.000425	0.000425
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: Involved in pre-mRNA splicing as component of the spliceosome (PubMed:11991638, PubMed:28502770, PubMed:28076346). Involved in transcription-coupled repair (TCR), transcription and pre-mRNA splicing (PubMed:10944529, PubMed:17981804). {ECO:0000269|PubMed:10944529, ECO:0000269|PubMed:11991638, ECO:0000269|PubMed:17981804, ECO:0000269|PubMed:28076346, ECO:0000269|PubMed:28502770}.;
Pathway: Spliceosome - Homo sapiens (human);DNA Repair;Metabolism of RNA;mRNA Splicing - Major Pathway;Formation of TC-NER Pre-Incision Complex;mRNA Splicing;Processing of Capped Intron-Containing Pre-mRNA;Dual incision in TC-NER;Gap-filling DNA repair synthesis and ligation in TC-NER;Transcription-Coupled Nucleotide Excision Repair (TC-NER);Nucleotide Excision Repair (Consensus)

Recessive Scores

pRec: 0.192

Intolerance Scores

loftool: 0.306
rvis_EVS: -1.37
rvis_percentile_EVS: 4.48

Haploinsufficiency Scores

pHI: 0.684
hipred: Y
hipred_score: 0.809
ghis: 0.594

Essentials

essential_gene_CRISPR: E
essential_gene_CRISPR2: E
essential_gene_gene_trap: E
gene_indispensability_pred: E
gene_indispensability_score: 0.921

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Xab2
Phenotype: mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); embryo phenotype;

Gene ontology

Biological process: generation of catalytic spliceosome for first transesterification step;mRNA splicing, via spliceosome;blastocyst development;transcription-coupled nucleotide-excision repair;transcription, DNA-templated;cerebral cortex development
Cellular component: Prp19 complex;nucleus;nucleoplasm;membrane;U2-type catalytic step 2 spliceosome;catalytic step 2 spliceosome;post-mRNA release spliceosomal complex
Molecular function: protein binding