TSGA10

testis specific 10

Basic information

Region (hg38): 2:98997261-99154964

Links

ENSG00000135951 ∙ NCBI:80705 ∙ OMIM:607166 ∙ HGNC:14927 ∙ Uniprot:Q9BZW7 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• spermatogenic failure 26 (Limited), mode of inheritance: Unknown

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Spermatogenic failure 26	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Genitourinary	28905369

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TSGA10 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TSGA10 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				5	2	7
missense			38			38
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)				1		1
splice region				3		3
non coding			2		3	5
Total	0	0	40	6	5

Variants in TSGA10

This is a list of pathogenic ClinVar variants found in the TSGA10 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-99018201-C-T		not specified	Uncertain significance (Oct 17, 2023)
2-99018212-C-T		not specified	Uncertain significance (May 09, 2022)
2-99018239-T-C		not specified	Uncertain significance (Nov 03, 2022)
2-99018243-G-A		not specified	Uncertain significance (Mar 11, 2022)
2-99018248-C-T		not specified	Uncertain significance (May 04, 2023)
2-99018249-G-A		not specified	Uncertain significance (Nov 28, 2023)
2-99018341-G-A		not specified	Uncertain significance (Sep 26, 2023)
2-99018545-C-A		not specified	Uncertain significance (Mar 11, 2024)
2-99018545-C-T		not specified	Uncertain significance (Jan 18, 2022)
2-99018594-G-T		not specified	Uncertain significance (Oct 26, 2021)
2-99020305-G-A		not specified	Uncertain significance (Aug 14, 2023)
2-99020363-T-A		not specified	Uncertain significance (Jan 16, 2024)
2-99020376-T-C		not specified	Uncertain significance (Jan 02, 2024)
2-99035324-T-A		not specified	Uncertain significance (Jun 17, 2024)
2-99035334-C-T		not specified	Uncertain significance (Jan 10, 2022)
2-99065002-A-C			Benign (Jun 19, 2018)
2-99065010-G-C		not specified	Uncertain significance (Nov 18, 2022)
2-99065048-C-T		not specified	Uncertain significance (May 17, 2023)
2-99068884-A-C		TSGA10-related disorder	Benign/Likely benign (Aug 01, 2024)
2-99068934-T-C		not specified	Uncertain significance (Oct 13, 2023)
2-99068940-A-T		not specified	Uncertain significance (Oct 20, 2021)
2-99068970-T-C		not specified	Uncertain significance (Mar 20, 2023)
2-99068992-A-T		not specified	Uncertain significance (Jul 05, 2022)
2-99069003-GA-G			Likely benign (Oct 01, 2022)
2-99071701-T-C		TSGA10-related disorder	Likely benign (Feb 01, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TSGA10	protein_coding	protein_coding	ENST00000393483	16	157704

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.110	0.890	125667	0	78	125745	0.000310

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.751	330	371	0.890	0.0000196	4638
Missense in Polyphen		72	92.946	0.77465		1331
Synonymous	2.06	91	120	0.760	0.00000558	1234
Loss of Function	4.65	11	44.5	0.247	0.00000285	487

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000308	0.000301
Ashkenazi Jewish	0.000216	0.000198
East Asian	0.000176	0.000163
Finnish	0.000105	0.0000924
European (Non-Finnish)	0.000475	0.000457
Middle Eastern	0.000176	0.000163
South Asian	0.000269	0.000261
Other	0.000348	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays a role in spermatogenesis (PubMed:28905369). When overexpressed, prevents nuclear localization of HIF1A (By similarity). {ECO:0000250|UniProtKB:Q6NY15, ECO:0000269|PubMed:28905369}.
• Disease: DISEASE: Spermatogenic failure 26 (SPGF26) [MIM:617961]: An autosomal recessive infertility disorder caused by spermatogenesis defects that result in acephalic spermatozoa. {ECO:0000269|PubMed:28905369}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Intolerance Scores

• loftool: 0.527
• rvis_EVS: -0.51
• rvis_percentile_EVS: 21.65

Haploinsufficiency Scores

• pHI: 0.455
• hipred: N
• hipred_score: 0.474
• ghis: 0.531

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.932

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tsga10

Gene ontology

• Biological process: spermatogenesis;cell projection assembly
• Cellular component: cellular_component;centriole;motile cilium;neuron projection
• Molecular function: molecular_function;protein binding