TRA2A

transformer 2 alpha homolog, the group of RNA binding motif containing

Basic information

Region (hg38): 7:23504779-23532041

Links

ENSG00000164548 ∙ NCBI:29896 ∙ OMIM:602718 ∙ HGNC:16645 ∙ Uniprot:Q13595 ∙ 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 TRA2A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TRA2A 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			13			13
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	13	0	0

Variants in TRA2A

This is a list of pathogenic ClinVar variants found in the TRA2A region.

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

Position	Type	Phenotype	Significance	ClinVar
7-23505772-C-T		not specified	Uncertain significance (Oct 30, 2023)
7-23506153-T-C		not specified	Uncertain significance (Jan 26, 2022)
7-23506241-C-T		not specified	Uncertain significance (Mar 07, 2024)
7-23506255-C-A		not specified	Uncertain significance (Mar 18, 2024)
7-23507436-T-C		not specified	Uncertain significance (Feb 08, 2023)
7-23516409-C-T		not specified	Uncertain significance (Oct 26, 2021)
7-23516418-C-T		not specified	Uncertain significance (Sep 22, 2022)
7-23516422-G-A		not specified	Uncertain significance (Feb 13, 2023)
7-23516428-A-G		not specified	Uncertain significance (Sep 23, 2023)
7-23516439-T-C		not specified	Uncertain significance (Aug 16, 2021)
7-23516465-A-T		not specified	Uncertain significance (Jun 11, 2024)
7-23516466-T-A		not specified	Uncertain significance (Jun 11, 2024)
7-23516473-G-A		not specified	Uncertain significance (Jan 02, 2024)
7-23516499-C-T		not specified	Uncertain significance (Jan 02, 2024)
7-23521743-T-C		not specified	Uncertain significance (Apr 25, 2023)
7-23521767-C-T		not specified	Uncertain significance (Dec 21, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TRA2A	protein_coding	protein_coding	ENST00000297071	8	27262

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00952	0.990	125731	0	16	125747	0.0000636

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.69	115	179	0.644	0.0000113	1760
Missense in Polyphen		10	32.462	0.30806		365
Synonymous	-0.224	60	57.8	1.04	0.00000305	587
Loss of Function	3.08	8	24.4	0.328	0.00000210	212

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000905	0.0000904
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000892	0.0000879
Middle Eastern	0.000109	0.000109
South Asian	0.0000327	0.0000327
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Sequence-specific RNA-binding protein which participates in the control of pre-mRNA splicing. {ECO:0000269|PubMed:9546399}.
• Pathway: Spliceosome - Homo sapiens (human) (Consensus)

Intolerance Scores

• loftool: 0.662
• rvis_EVS: -0.32
• rvis_percentile_EVS: 31.46

Haploinsufficiency Scores

• hipred: Y
• hipred_score: 0.704
• ghis: 0.682

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.889

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tra2a

Gene ontology

• Biological process: mRNA splicing, via spliceosome;positive regulation of mRNA splicing, via spliceosome
• Cellular component: nucleus;nucleolus;intracellular membrane-bounded organelle;ribonucleoprotein complex
• Molecular function: RNA binding