TSGA13

testis specific 13

Basic information

Region (hg38): 7:130668643-130687432

Links

ENSG00000213265 ∙ NCBI:114960 ∙ ∙ HGNC:12369 ∙ Uniprot:Q96PP4 ∙ 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 TSGA13 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TSGA13 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			15	1		16
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	15	1	0

Variants in TSGA13

This is a list of pathogenic ClinVar variants found in the TSGA13 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-130669028-T-G		not specified	Uncertain significance (Nov 08, 2022)
7-130669047-C-A		not specified	Uncertain significance (Nov 08, 2022)
7-130669061-C-G		not specified	Uncertain significance (Apr 12, 2022)
7-130669067-G-A		not specified	Uncertain significance (Jan 17, 2023)
7-130669168-G-T		not specified	Uncertain significance (Feb 27, 2024)
7-130671678-C-T		not specified	Uncertain significance (Dec 21, 2022)
7-130671732-A-G		not specified	Uncertain significance (May 11, 2022)
7-130671775-T-C		not specified	Uncertain significance (Jan 04, 2022)
7-130672749-C-T		not specified	Uncertain significance (Aug 13, 2021)
7-130672770-G-A		not specified	Likely benign (Apr 18, 2023)
7-130672861-G-A		not specified	Uncertain significance (Jun 30, 2022)
7-130679195-G-T		not specified	Uncertain significance (Sep 23, 2023)
7-130679211-G-T		not specified	Uncertain significance (Dec 28, 2023)
7-130679258-G-A		not specified	Uncertain significance (Mar 01, 2023)
7-130680951-T-C		not specified	Uncertain significance (Aug 13, 2021)
7-130683672-C-G		not specified	Uncertain significance (Jan 24, 2024)
7-130685195-G-T		not specified	Uncertain significance (Mar 19, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TSGA13	protein_coding	protein_coding	ENST00000456951	7	18781

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
7.39e-10	0.0771	125721	0	27	125748	0.000107

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.466	165	149	1.11	0.00000726	1812
Missense in Polyphen		9	7.3527	1.224		64
Synonymous	0.601	52	57.8	0.899	0.00000296	498
Loss of Function	-0.0204	14	13.9	1.01	6.70e-7	175

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000182	0.000182
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000552	0.0000527
Middle Eastern	0.00	0.00
South Asian	0.000504	0.000490
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0914

Intolerance Scores

• rvis_EVS: -0.58
• rvis_percentile_EVS: 18.44

Haploinsufficiency Scores

• pHI: 0.212
• hipred: N
• hipred_score: 0.123
• ghis: 0.495

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.253

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tsga13
• Phenotype: normal phenotype