TSNAX

translin associated factor X, the group of Endoribonucleases

Basic information

Region (hg38): 1:231528541-231566524

Links

ENSG00000116918 ∙ NCBI:7257 ∙ OMIM:602964 ∙ HGNC:12380 ∙ Uniprot:Q99598 ∙ 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 TSNAX gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TSNAX 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					2	2
missense			9		1	10
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	9	0	3

Variants in TSNAX

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

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

Position	Type	Phenotype	Significance	ClinVar
1-231529260-G-C		not specified	Uncertain significance (May 17, 2023)
1-231529288-A-G			Benign (Mar 31, 2018)
1-231529292-C-T			Benign (Apr 16, 2018)
1-231561120-G-A			Benign (Jun 14, 2018)
1-231561210-A-G			Benign (Jun 26, 2018)
1-231561217-A-G		not specified	Uncertain significance (May 03, 2023)
1-231564588-G-A		not specified	Uncertain significance (Jun 26, 2023)
1-231564688-A-T		not specified	Uncertain significance (Nov 10, 2022)
1-231564696-C-T		not specified	Uncertain significance (Jan 24, 2023)
1-231564697-G-A		not specified	Uncertain significance (Feb 21, 2024)
1-231564744-G-A		not specified	Uncertain significance (Aug 04, 2023)
1-231564783-G-A		not specified	Uncertain significance (Oct 29, 2021)
1-231564841-A-G		not specified	Uncertain significance (Dec 27, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TSNAX	protein_coding	protein_coding	ENST00000366639	6	37872

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.489	0.510	125727	0	20	125747	0.0000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.30	107	152	0.703	0.00000735	1925
Missense in Polyphen		24	41.511	0.57816		521
Synonymous	-0.333	57	53.9	1.06	0.00000256	516
Loss of Function	2.82	3	14.7	0.205	7.80e-7	182

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000202	0.000202
Ashkenazi Jewish	0.000119	0.0000992
East Asian	0.00	0.00
Finnish	0.0000925	0.0000924
European (Non-Finnish)	0.0000823	0.0000791
Middle Eastern	0.00	0.00
South Asian	0.000131	0.000131
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Acts in combination with TSN as an endonuclease involved in the activation of the RNA-induced silencing complex (RISC). Possible role in spermatogenesis. {ECO:0000269|PubMed:12036294, ECO:0000269|PubMed:21552258}.
• Pathway: Gene expression (Transcription);Small interfering RNA (siRNA) biogenesis;Gene Silencing by RNA (Consensus)

Recessive Scores

• pRec: 0.147

Intolerance Scores

• loftool: 0.232
• rvis_EVS: 0.01
• rvis_percentile_EVS: 54.95

Haploinsufficiency Scores

• pHI: 0.0512
• hipred: Y
• hipred_score: 0.633
• ghis: 0.583

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.976

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tsnax

Gene ontology

• Biological process: multicellular organism development;spermatogenesis;protein transport;cell differentiation;RNA phosphodiester bond hydrolysis, endonucleolytic
• Cellular component: nucleus;cytoplasm;Golgi apparatus;cytosol;perinuclear region of cytoplasm
• Molecular function: DNA binding;single-stranded DNA binding;RNA binding;endoribonuclease activity;protein binding;protein transporter activity;A2A adenosine receptor binding;sequence-specific DNA binding;protein-containing complex binding;metal ion binding