TSGA13

Summary

TSGA13 (testis specific 13, HGNC:12369) is a protein-coding gene on chromosome 7q32.2, encoding Testis-specific gene 13 protein (Q96PP4).

At a glance

• GWAS associations: 4
• Clinical variants (ClinVar): 34 total
• MANE Select transcript: NM_052933

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:12369
Approved symbol	TSGA13
Name	testis specific 13
Location	7q32.2
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000213265
Ensembl biotype	protein_coding
Entrez	114960

Gene structure

Transcript identifiers

Ensembl transcripts: 4 — 4 protein_coding

ENST00000356588, ENST00000438346, ENST00000443954, ENST00000456951

RefSeq mRNA: 2 — MANE Select: NM_052933 NM_001304968, NM_052933

CCDS: CCDS5824

Canonical transcript exons

ENST00000356588 — 8 exons

Exon	Start	End
ENSE00001039916	130671661	130671788
ENSE00001039945	130683594	130683672
ENSE00001039949	130672734	130672876
ENSE00001039952	130679155	130679367
ENSE00001224984	130686262	130686545
ENSE00001384832	130668643	130669183
ENSE00001395468	130685188	130685360
ENSE00003786621	130680946	130681017

Expression profiles

Bgee: expression breadth broad, 18 present calls, max score 78.14.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.0027 / max 2.2548, expressed in 3 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
86160	0.0027	3

Top tissues by expression

210 total, by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
left testis	UBERON:0004533	78.14	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	77.55	silver quality
right testis	UBERON:0004534	77.21	gold quality
testis	UBERON:0000473	75.76	gold quality
mucosa of paranasal sinus	UBERON:0005030	68.01	gold quality
sperm	CL:0000019	64.99	silver quality
cartilage tissue	UBERON:0002418	58.67	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	58.26	gold quality
pericardium	UBERON:0002407	58.20	silver quality
heart right ventricle	UBERON:0002080	56.38	gold quality
skeletal muscle tissue of biceps brachii	UBERON:0004502	55.79	gold quality
pons	UBERON:0000988	55.61	gold quality
lower lobe of lung	UBERON:0008949	55.52	silver quality
biceps brachii	UBERON:0001507	55.04	gold quality
vena cava	UBERON:0004087	54.46	gold quality
parotid gland	UBERON:0001831	54.43	gold quality
trabecular bone tissue	UBERON:0002483	53.31	gold quality
decidua	UBERON:0002450	52.89	gold quality
postcentral gyrus	UBERON:0002581	52.13	gold quality
buccal mucosa cell	CL:0002336	51.56	gold quality
adult organism	UBERON:0007023	51.55	silver quality
germinal epithelium of ovary	UBERON:0001304	51.02	gold quality
vastus lateralis	UBERON:0001379	50.88	gold quality
parietal lobe	UBERON:0001872	50.67	gold quality
quadriceps femoris	UBERON:0001377	50.64	gold quality
entorhinal cortex	UBERON:0002728	49.85	gold quality
sural nerve	UBERON:0015488	49.00	gold quality
mammalian vulva	UBERON:0000997	48.78	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	48.41	gold quality
skeletal muscle tissue	UBERON:0001134	47.81	gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	4.23
E-GEOD-111727	no	252.30
E-MTAB-7303	no	12.27

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

6 targeting TSGA13, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-514B-5P	99.50	68.19	1766
HSA-MIR-4279	99.19	66.70	2437
HSA-MIR-6884-5P	99.10	64.50	1987
HSA-MIR-3619-5P	99.00	68.87	2308
HSA-MIR-214-3P	98.71	68.12	2128
HSA-MIR-3655	86.11	61.77	117

Literature-anchored findings (GeneRIF, showing 2)

• the data from the current study strongly suggest the association between TSGA13 and tumor malignancy. (PMID:26111495)
• Findings provide evidence for genetic association of the TSGA13 gene with total colonic aganglionosis, the most severe subtype of Hirschsprung disease. (PMID:31181311)

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Tsga13	ENSMUSG00000039032
rattus_norvegicus	Tsga13	ENSRNOG00000011108

Protein

Protein identifiers

Testis-specific gene 13 protein — Q96PP4 (reviewed: Q96PP4)

All UniProt accessions (3): C9JIG7, C9JVS7, Q96PP4

UniProt curated annotations — full annotation on UniProt →

Tissue specificity. Testis-specific.

RefSeq proteins (2): NP_001291897, NP_443165* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR029241	TSGA13	Family

Pfam: PF14994

UniProt features (3 total): chain 1, region of interest 1, compositionally biased region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q96PP4-F1	60.38	0.10

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 33 (showing top): GSE45365_NK_CELL_VS_CD11B_DC_UP, ACEVEDO_LIVER_CANCER_WITH_H3K27ME3_UP, chr7q32, CONRAD_GERMLINE_STEM_CELL, TST1_01, TEF_Q6, KOYAMA_SEMA3B_TARGETS_DN, GSE10273_HIGH_VS_LOW_IL7_TREATED_IRF4_8_NULL_PRE_BCELL_DN, GSE11924_TH1_VS_TH2_CD4_TCELL_DN, CTTTAAR_UNKNOWN, GSE17721_CTRL_VS_POLYIC_2H_BMDC_DN, GSE17721_CTRL_VS_POLYIC_12H_BMDC_UP, GSE17721_CTRL_VS_PAM3CSK4_1H_BMDC_DN, GSE17721_CTRL_VS_CPG_0.5H_BMDC_DN, DESCARTES_MAIN_FETAL_MUC13_DMBT1_POSITIVE_CELLS

GO Biological Process (0):

GO Molecular Function (1): protein binding (GO:0005515)

GO Cellular Component (0):

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
binding	1

Protein interactions and networks

STRING

690 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
TSGA13	COPG2	Q9UBF2	647
TSGA13	CPA4	Q9UI42	590
TSGA13	CPA5	Q8WXQ8	546
TSGA13	SSMEM1	Q8WWF3	541
TSGA13	MKLN1	Q9UL63	532
TSGA13	TMEM209	Q96SK2	475
TSGA13	GRB10	Q13322	462
TSGA13	KLHDC10	Q6PID8	451
TSGA13	GARIN1B	Q96KD3	446
TSGA13	CEP41	Q9BYV8	443
TSGA13	CPA2	P48052	420
TSGA13	MCPH1	Q8NEM0	384
TSGA13	KLF14	Q8TD94	380
TSGA13	ASCL2	Q99929	363
TSGA13	KCNQ1	P51787	353
TSGA13	DLK1	P15803	353

IntAct

6 interactions, top by confidence:

A	B	Type	Score
MLH1	TSGA13	psi-mi:“MI:0915”(physical association)	0.560
TSGA13	SCGB2A1	psi-mi:“MI:0914”(association)	0.530
TSGA13	MLH1	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (7): SCGB2A1 (Affinity Capture-MS), IGHA2 (Affinity Capture-MS), IGHA2 (Affinity Capture-MS), SCGB2A1 (Affinity Capture-MS), TSGA13 (Two-hybrid), SCGB2A1 (Affinity Capture-MS), IGHA2 (Affinity Capture-MS)

ESM2 similar proteins: A0A1B0GVB3, A0A1B0GVH6, A2RRY8, A4IGV6, A6NHR8, B3DHS1, E1B9I5, O74317, O95561, P03319, P03320, P0C9Z5, P0C9Z6, P10260, P36353, P40744, P40745, Q06616, Q09280, Q09424, Q2KIL1, Q2KIR0, Q32KT7, Q32LB6, Q3T028, Q3TTI8, Q496A3, Q5NC83, Q5SQS8, Q5XIU7, Q68FQ8, Q6DFB0, Q6ZNM6, Q6ZV65, Q811V6, Q8IWA6, Q8N9R6, Q8R0E5, Q8TAL5, Q8WTQ4

Diamond homologs: Q3T028, Q95JJ2, Q96PP4, Q9DA17

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

34 variants total. Per-class counts are floors (≥ shown; pagination cap):

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	30
Likely benign	1
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1253 predictions. Top by Δscore:

Variant	Effect	Δscore
7:130683589:CTTAC:C	donor_loss	1.0000
7:130683593:C:CA	donor_loss	1.0000
7:130685186:A:AC	donor_gain	1.0000
7:130685187:C:CC	donor_gain	1.0000
7:130685360:CCTGT:C	acceptor_loss	1.0000
7:130685361:CT:C	acceptor_loss	1.0000
7:130685362:T:G	acceptor_loss	1.0000
7:130668643:T:TA	donor_gain	0.9900
7:130671667:T:A	donor_gain	0.9900
7:130671790:T:C	acceptor_gain	0.9900
7:130672736:AAAC:A	donor_gain	0.9900
7:130672810:A:C	donor_gain	0.9900
7:130679201:T:A	donor_gain	0.9900
7:130683593:CCT:C	donor_gain	0.9900
7:130683670:AACCT:A	acceptor_loss	0.9900
7:130683671:ACC:A	acceptor_loss	0.9900
7:130683672:CCT:C	acceptor_loss	0.9900
7:130683674:T:A	acceptor_loss	0.9900
7:130685180:CTACA:C	donor_loss	0.9900
7:130685181:TACAT:T	donor_loss	0.9900
7:130685182:ACATA:A	donor_loss	0.9900
7:130685183:CAT:C	donor_loss	0.9900
7:130685184:ATA:A	donor_loss	0.9900
7:130685185:TACTT:T	donor_loss	0.9900
7:130685187:C:CG	donor_loss	0.9900
7:130685187:CTTG:C	donor_gain	0.9900
7:130685187:CTTGG:C	donor_gain	0.9900
7:130685248:T:C	donor_gain	0.9900
7:130685361:C:CC	acceptor_gain	0.9900
7:130669184:C:CC	acceptor_gain	0.9800

AlphaMissense

1818 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
7:130671785:A:C	F178L	0.982
7:130671785:A:T	F178L	0.982
7:130671787:A:G	F178L	0.982
7:130669068:G:C	F258L	0.969
7:130669068:G:T	F258L	0.969
7:130669070:A:G	F258L	0.969
7:130680988:A:C	F44L	0.969
7:130680988:A:T	F44L	0.969
7:130680990:A:G	F44L	0.969
7:130671767:G:C	F184L	0.961
7:130671767:G:T	F184L	0.961
7:130671769:A:G	F184L	0.961
7:130679236:G:C	N102K	0.957
7:130679236:G:T	N102K	0.957
7:130679239:G:C	N101K	0.956
7:130679239:G:T	N101K	0.956
7:130679252:A:G	L97P	0.953
7:130671786:A:G	F178S	0.952
7:130671695:A:C	F208L	0.947
7:130671695:A:T	F208L	0.947
7:130671697:A:G	F208L	0.947
7:130672736:A:C	F176L	0.942
7:130672736:A:T	F176L	0.942
7:130672738:A:G	F176L	0.942
7:130671788:C:A	R177S	0.936
7:130671788:C:G	R177S	0.936
7:130669046:A:G	W266R	0.926
7:130669046:A:T	W266R	0.926
7:130671768:A:G	F184S	0.926
7:130679240:T:A	N101I	0.924

dbSNP variants (sampled 300 via entrez): RS1000388437 (7:130678101 G>A), RS1000636205 (7:130672229 A>G), RS1000938636 (7:130682011 G>A), RS1001384129 (7:130668858 C>T), RS1001400779 (7:130688510 T>A,C), RS1001625818 (7:130685007 A>G), RS1001974550 (7:130673108 T>A), RS1002480118 (7:130669939 G>A,T), RS1002645049 (7:130675675 G>A), RS1003002892 (7:130675941 A>G,T), RS1003054345 (7:130670170 G>A,C), RS1003174686 (7:130686663 A>G), RS1003486816 (7:130668792 C>G), RS1003591756 (7:130674572 G>A), RS1003698856 (7:130686459 G>A)

Disease associations

OMIM: gene `` | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

4 associations (top):

Study	Trait	p-value
GCST002553_9	Pancreatic cancer	3.000000e-12
GCST005958_14	Waist-to-hip ratio adjusted for BMI (age >50)	1.000000e-07
GCST005962_34	Waist-to-hip ratio adjusted for BMI x sex x age interaction (4df test)	6.000000e-07
GCST008158_135	Body mass index	9.000000e-06

EFO canonical traits (4, from GWAS)

EFO ID	Trait name
EFO:0007788	BMI-adjusted waist-hip ratio
EFO:0008007	age at assessment
EFO:0008343	sex interaction measurement
EFO:0004340	body mass index

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

6 total (human), top 6 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
bisphenol A	affects cotreatment, increases methylation	1
CGP 52608	affects binding, increases reaction	1
Resveratrol	affects cotreatment, decreases expression	1
Fulvestrant	increases methylation, affects cotreatment	1
Benzo(a)pyrene	increases methylation	1
Copper	affects cotreatment, decreases expression	1

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.