XAB2

protein-coding

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

Gene summary

Involved in DNA-templated transcription; mRNA splicing, via spliceosome; and transcription-coupled nucleotide-excision repair. Located in nucleoplasm. Part of U2-type catalytic step 2 spliceosome. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_020196.3

Inheritance

—

ClinVar variants

U:156

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.18

Max pathogenic AF

—

Genomic locus

chr19:7,619,525-7,629,545

External References & Databases

Ensembl (ENSG00000076924)

Transcript & Mutation Effects

hg38 • Region Span ~10.0 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 XAB2 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 139

not providedTotal: 3

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_020196.3. 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			5 clinvar			5
missense			144 clinvar			144
nonsense						0
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			6 clinvar			6
Total	0	0	156	0	0	156

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_020196.3	RefSeq	NP_064581.2	19	MANE Select
ENST00000358368.5	Ensembl	ENSP00000351137.3	19	MANE Select
ENST00000855696.1	Ensembl	ENSP00000525755.1	19	Standard
ENST00000855696.2	Ensembl	ENSP00000525755.1	19	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Spliceosome - Homo sapiens (human)
DNA Repair
Metabolism of RNA
mRNA Splicing - Major Pathway
Formation of TC-NER Pre-Incision Complex

Biological Process

generation of catalytic spliceosome for first transesterification step
mRNA splicing, via spliceosome
blastocyst development
transcription-coupled nucleotide-excision repair
transcription, DNA-templated

Molecular Function

protein binding

Cellular Component

Prp19 complex
nucleus
nucleoplasm
membrane
U2-type catalytic step 2 spliceosome

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000358368
Coding exons: 19
Length: 10041
Individuals with no LoFs: 125718
Homozygous LoFs: 0
Heterozygous LoFs: 30
Defined: 125748
p: 0.000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.94	471	605	0.779	0.0000450	5537
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0.000034	0.000029	rare
Ashkenazi Jewish	0.00010	0.000099	rare
East Asian	0.000055	0.000054	rare
Finnish	0.00014	0.00014	rare
European (Non-Finnish)	0.000088	0.000088	rare
South Asian	0.00042	0.00042	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

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}.;

Recessive Scores

pRec: 0.192

Intolerance Scores

LoFtool: 0.306
RVIS EVS: -1.37
RVIS percentile EVS: 4.48

Essentials

Essential (CRISPR): E
Essential (CRISPR2): E
Essential (gene trap): E
Indispensability pred.: E
Indispensability score: 0.921

Gene Damage Prediction

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