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GeneBe

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

ENSG00000136527NCBI:6434OMIM:602719HGNC:10781Uniprot:P62995AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

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.

  • not provided (3 variants)
  • Inborn genetic diseases (2 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
4
clinvar
4
nonsense
0
start loss
0
frameshift
1
clinvar
1
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
0
Total 0 0 5 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)2582209
3-185919448-A-C Inborn genetic diseases Uncertain significance (Jul 27, 2022)2304078
3-185922047-G-A Uncertain significance (Dec 26, 2021)2412961
3-185925504-T-C Inborn genetic diseases Uncertain significance (Dec 31, 2023)3181722
3-185925515-GT-G Uncertain significance (Mar 24, 2023)2582049
3-185925552-C-T Inborn genetic diseases Uncertain significance (Aug 11, 2022)2210707
3-185926600-C-T TRA2B-associated epileptic encephalopathy Pathogenic (Apr 02, 2023)2579119

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
TRA2Bprotein_codingprotein_codingENST00000453386 922231
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.9930.00688125736051257410.0000199
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense3.50601990.3020.00001341816
Missense in Polyphen130.6160.032663361
Synonymous0.03825959.40.9940.00000291585
Loss of Function3.86119.30.05190.00000125213

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.00002890.0000289
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.000.00
European (Non-Finnish)0.00003600.0000352
Middle Eastern0.000.00
South Asian0.000.00
Other0.000.00

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

AllRecessiveDominant
MendelianMediumLowMedium
Primary ImmunodeficiencyMediumLowMedium
CancerMediumMediumMedium

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