TRA2B

transformer 2 beta homolog, the group of RNA binding motif containing|Protein phosphatase 1 regulatory subunits

Basic information

Region (hg38): 3:185914557-185938103

Previous symbols: [ "SFRS10" ]

Links

ENSG00000136527 ∙ NCBI:6434 ∙ OMIM:602719 ∙ HGNC:10781 ∙ Uniprot:P62995 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• complex neurodevelopmental disorder (Moderate), mode of inheritance: AD

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TRA2B gene.

• TRA2B-associated epileptic encephalopathy (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TRA2B 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						0
missense			5			5
nonsense						0
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)	1					1
splice region						0
non coding						0
Total	1	0	6	0	0

Variants in TRA2B

This is a list of pathogenic ClinVar variants found in the TRA2B region.

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

Position	Type	Phenotype	Significance	ClinVar
3-185918424-G-A			Uncertain significance (Mar 31, 2023)
3-185919448-A-C		Inborn genetic diseases	Uncertain significance (Jul 27, 2022)
3-185922047-G-A			Uncertain significance (Dec 26, 2021)
3-185925504-T-C		Inborn genetic diseases	Uncertain significance (Dec 31, 2023)
3-185925515-GT-G			Uncertain significance (Mar 24, 2023)
3-185925552-C-T		Inborn genetic diseases	Uncertain significance (Aug 11, 2022)
3-185926600-C-T		TRA2B-associated epileptic encephalopathy	Pathogenic (Apr 02, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TRA2B	protein_coding	protein_coding	ENST00000453386	9	22231

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.993	0.00688	125736	0	5	125741	0.0000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.50	60	199	0.302	0.0000134	1816
Missense in Polyphen		1	30.616	0.032663		361
Synonymous	0.0382	59	59.4	0.994	0.00000291	585
Loss of Function	3.86	1	19.3	0.0519	0.00000125	213

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000360	0.0000352
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Sequence-specific RNA-binding protein which participates in the control of pre-mRNA splicing. Can either activate or suppress exon inclusion. Acts additively with RBMX to promote exon 7 inclusion of the survival motor neuron SMN2. Activates the splicing of MAPT/Tau exon 10. Alters pre-mRNA splicing patterns by antagonizing the effects of splicing regulators, like RBMX. Binds to the AG-rich SE2 domain in the SMN exon 7 RNA. Binds to pre- mRNA. {ECO:0000269|PubMed:12165565, ECO:0000269|PubMed:12761049, ECO:0000269|PubMed:15009664, ECO:0000269|PubMed:9546399}.
• Pathway: Spliceosome - Homo sapiens (human);mRNA Processing;Metabolism of RNA;mRNA Splicing - Major Pathway;mRNA Splicing;Processing of Capped Intron-Containing Pre-mRNA (Consensus)

Recessive Scores

• pRec: 0.171

Intolerance Scores

• loftool: 0.119
• rvis_EVS: -0.05
• rvis_percentile_EVS: 49.39

Haploinsufficiency Scores

• pHI: 0.753
• hipred: Y
• hipred_score: 0.775
• ghis: 0.724

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.609

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tra2b
• Phenotype: growth/size/body region phenotype; homeostasis/metabolism phenotype; normal 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); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); embryo phenotype

Gene ontology

• Biological process: RNA splicing, via transesterification reactions;regulation of alternative mRNA splicing, via spliceosome;mRNA splicing, via spliceosome;cerebral cortex regionalization;regulation of RNA splicing;positive regulation of mRNA splicing, via spliceosome;protein complex oligomerization;cellular response to glucose stimulus;embryonic brain development
• Cellular component: nucleus;nuclear inner membrane;nucleoplasm;spliceosomal complex;ribonucleoprotein complex
• Molecular function: RNA binding;mRNA binding;protein binding;protein domain specific binding;pre-mRNA binding;identical protein binding