TSNAXIP1

translin associated factor X interacting protein 1, the group of TSNAXIP1 domain containing

Basic information

Region (hg38): 16:67806765-67832148

Links

ENSG00000102904 ∙ NCBI:55815 ∙ OMIM:607720 ∙ HGNC:18586 ∙ Uniprot:Q2TAA8 ∙ 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 TSNAXIP1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TSNAXIP1 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			48	3		51
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	48	3	0

Variants in TSNAXIP1

This is a list of pathogenic ClinVar variants found in the TSNAXIP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-67820878-C-T		not specified	Uncertain significance (Apr 20, 2024)
16-67820924-G-C		not specified	Uncertain significance (Aug 21, 2023)
16-67820933-A-G		not specified	Uncertain significance (Jun 18, 2021)
16-67820945-G-A		not specified	Uncertain significance (Feb 08, 2023)
16-67821121-C-T		not specified	Uncertain significance (Sep 16, 2021)
16-67823702-C-T		not specified	Uncertain significance (May 18, 2023)
16-67824607-C-A		not specified	Uncertain significance (Jan 26, 2023)
16-67824625-C-T		not specified	Uncertain significance (Sep 27, 2022)
16-67824628-A-G		not specified	Uncertain significance (Jan 29, 2024)
16-67824690-T-C		not specified	Likely benign (Oct 12, 2022)
16-67824711-A-G		not specified	Uncertain significance (Dec 14, 2023)
16-67824735-C-T		not specified	Uncertain significance (May 20, 2024)
16-67825197-G-A		not specified	Uncertain significance (Jun 02, 2024)
16-67825231-T-G		not specified	Uncertain significance (Nov 15, 2023)
16-67825260-G-T		not specified	Uncertain significance (Dec 20, 2023)
16-67825269-C-T		not specified	Uncertain significance (Apr 17, 2023)
16-67825669-A-G		not specified	Likely benign (May 05, 2023)
16-67825675-G-T		not specified	Uncertain significance (Jan 06, 2023)
16-67825702-G-C		not specified	Uncertain significance (Nov 23, 2021)
16-67825717-C-T		not specified	Uncertain significance (Sep 20, 2023)
16-67825733-G-A		not specified	Uncertain significance (Dec 12, 2023)
16-67825736-C-T		not specified	Uncertain significance (Feb 21, 2024)
16-67825757-T-C		not specified	Uncertain significance (Aug 12, 2022)
16-67825762-G-C		not specified	Uncertain significance (Jan 26, 2023)
16-67825798-G-A		not specified	Uncertain significance (Nov 12, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TSNAXIP1	protein_coding	protein_coding	ENST00000388833	14	25384

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.28e-29	0.0000105	124393	2	1353	125748	0.00540

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.468	400	375	1.07	0.0000222	4364
Missense in Polyphen		155	137.83	1.1246		1688
Synonymous	0.0233	147	147	0.998	0.00000865	1195
Loss of Function	-0.871	40	34.5	1.16	0.00000171	397

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0184	0.0165
Ashkenazi Jewish	0.00190	0.00189
East Asian	0.00550	0.00507
Finnish	0.00407	0.00384
European (Non-Finnish)	0.00626	0.00596
Middle Eastern	0.00550	0.00507
South Asian	0.00241	0.00232
Other	0.00374	0.00359

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Possible role in spermatogenesis. {ECO:0000250|UniProtKB:Q99P25}.

Recessive Scores

• pRec: 0.107

Intolerance Scores

• loftool: 0.268
• rvis_EVS: -0.49
• rvis_percentile_EVS: 22.7

Haploinsufficiency Scores

• pHI: 0.138
• hipred: N
• hipred_score: 0.200
• ghis: 0.543

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.464

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tsnaxip1

Gene ontology

• Biological process: multicellular organism development;spermatogenesis;biological_process;cell differentiation
• Cellular component: cellular_component;perinuclear region of cytoplasm
• Molecular function: molecular_function