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.

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.

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			52			52
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)			1			1
splice region						0
non coding				1		1
Total	0	0	53	1	1

Variants in XAB2

This is a list of pathogenic ClinVar variants found in the XAB2 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-7619602-C-T		not specified	Uncertain significance (Feb 14, 2024)
19-7619608-A-G		not specified	Uncertain significance (Jun 16, 2023)
19-7619621-G-A		not specified	Uncertain significance (May 02, 2023)
19-7619624-C-T		not specified	Uncertain significance (Aug 25, 2021)
19-7619641-C-A		not specified	Uncertain significance (Aug 14, 2024)
19-7619642-G-A		not specified	Uncertain significance (Jun 26, 2024)
19-7619765-T-C		not specified	Uncertain significance (Jun 01, 2023)
19-7619783-C-A		not specified	Uncertain significance (Oct 12, 2024)
19-7619786-C-T		not specified	Uncertain significance (Sep 08, 2024)
19-7619827-T-C		not specified	Uncertain significance (Jun 07, 2023)
19-7619842-C-T		not specified	Uncertain significance (Oct 22, 2021)
19-7619950-C-T		not specified	Uncertain significance (Jan 17, 2024)
19-7619958-A-G		not specified	Uncertain significance (Nov 10, 2024)
19-7619971-C-T		not specified	Uncertain significance (May 12, 2024)
19-7619979-G-A		not specified	Uncertain significance (Jun 16, 2024)
19-7619988-C-T		not specified	Uncertain significance (Oct 27, 2022)
19-7619989-G-A		not specified	Uncertain significance (Feb 23, 2023)
19-7620003-G-A		not specified	Uncertain significance (Apr 15, 2024)
19-7620040-C-T		not specified	Uncertain significance (Feb 17, 2022)
19-7620076-C-A			Uncertain significance (Oct 16, 2018)
19-7620283-G-A		not specified	Uncertain significance (May 27, 2022)
19-7620361-C-T		not specified	Uncertain significance (Apr 09, 2024)
19-7620412-A-G		not specified	Uncertain significance (Feb 24, 2022)
19-7620425-T-G		not specified	Uncertain significance (Aug 09, 2021)
19-7620436-G-A		not specified	Uncertain significance (Jan 20, 2023)

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