TCTA

T cell leukemia translocation altered

Basic information

Region (hg38): 3:49412211-49416476

Links

ENSG00000145022 ∙ NCBI:6988 ∙ OMIM:600690 ∙ HGNC:11692 ∙ Uniprot:P57738 ∙ 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 TCTA gene.

• Inborn genetic diseases (2 variants)

Variants pathogenicity by type

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

Variants in TCTA

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

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

Position	Type	Phenotype	Significance	ClinVar
3-49412460-G-A		not specified	Uncertain significance (Jan 19, 2024)
3-49412551-T-C		not specified	Uncertain significance (Oct 25, 2023)
3-49412633-C-A		not specified	Uncertain significance (Nov 15, 2023)
3-49413056-G-A		not specified	Uncertain significance (Dec 14, 2021)
3-49413064-G-A		not specified	Uncertain significance (Sep 14, 2022)
3-49413102-C-A		not specified	Uncertain significance (Jan 17, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TCTA	protein_coding	protein_coding	ENST00000273590	3	4270

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000463	0.446	125737	0	11	125748	0.0000437

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0760	58	59.7	0.972	0.00000309	648
Missense in Polyphen		30	27.659	1.0846		323
Synonymous	-0.832	33	27.5	1.20	0.00000158	217
Loss of Function	0.0938	5	5.23	0.956	2.27e-7	52

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000235	0.000235
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000176	0.0000176
Middle Eastern	0.000109	0.000109
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be required for cellular fusion during osteoclastogenesis. {ECO:0000269|PubMed:19560569}.

Recessive Scores

• pRec: 0.141

Intolerance Scores

• loftool: 0.381
• rvis_EVS: 0.13
• rvis_percentile_EVS: 62.74

Haploinsufficiency Scores

• pHI: 0.459
• hipred: N
• hipred_score: 0.325
• ghis: 0.516

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.231

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tcta

Gene ontology

• Biological process: negative regulation of osteoclast differentiation;osteoclast fusion
• Cellular component: integral component of membrane
• Molecular function: molecular_function