TSNAX

protein-coding

translin associated factor X, the group of Endoribonucleases

Gene summary

This gene encodes a protein which specifically interacts with translin, a DNA-binding protein that binds consensus sequences at breakpoint junctions of chromosomal translocations. The encoded protein contains bipartite nuclear targeting sequences that may provide nuclear transport for translin, which lacks any nuclear targeting motifs. [provided by RefSeq, Jul 2008]

MANE transcript

NM_005999.3

Inheritance

—

ClinVar variants

U:29B:3

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.2

Max pathogenic AF

—

Genomic locus

chr1:231,528,541-231,566,524

External References & Databases

Ensembl (ENSG00000116918)

Transcript & Mutation Effects

hg38 • Region Span ~38.0 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to TSNAX variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 28

not providedTotal: 4

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_005999.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous					2 clinvar	2
missense			28 clinvar		1 clinvar	29
nonsense						0
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)						0
Total	0	0	29	0	3	32

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 26 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_005999.3	RefSeq	NP_005990.1	6	MANE Select
ENST00000366639.9	Ensembl	ENSP00000355599.3	6	MANE Select
ENST00000413309.3	Ensembl	ENSP00000397537.1	5	Standard
ENST00000903833.1	Ensembl	ENSP00000573892.1	6	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Gene expression (Transcription)
Small interfering RNA (siRNA) biogenesis
Gene Silencing by RNA

Biological Process

multicellular organism development
spermatogenesis
protein transport
cell differentiation
RNA phosphodiester bond hydrolysis, endonucleolytic

Molecular Function

DNA binding
single-stranded DNA binding
RNA binding
endoribonuclease activity
protein binding

Cellular Component

nucleus
cytoplasm
Golgi apparatus
cytosol
perinuclear region of cytoplasm

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000366639
Coding exons: 6
Length: 37872
Individuals with no LoFs: 125727
Homozygous LoFs: 0
Heterozygous LoFs: 20
Defined: 125747
p: 0.0000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.30	107	152	0.703	0.00000735	1925
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00012	0.00012	rare
Latino/Admixed American	0.000079	0.000058	rare
Ashkenazi Jewish	0.00012	0.000099	rare
East Asian	0	0.0	absent
Finnish	0.000092	0.000092	rare
European (Non-Finnish)	0.000082	0.000079	rare
South Asian	0.00013	0.00013	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

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}.;

Recessive Scores

pRec: 0.147

Intolerance Scores

LoFtool: 0.232
RVIS EVS: 0.01
RVIS percentile EVS: 54.95

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.976

Gene Damage Prediction

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