TSGA10

protein-coding

testis specific 10

Gene summary

Predicted to enable structural molecule activity. Predicted to be involved in spermatogenesis. Located in centriole. Implicated in spermatogenic failure 26. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_025244.4

Inheritance

ClinVar variants

P:2U:92B:10

Top phenotype

Spermatogenic failure 26

gnomAD constraint

pLI —, LoF o/e 0.25

Max pathogenic AF

—

Genomic locus

chr2:98,997,261-99,154,964

External References & Databases

Ensembl (ENSG00000135951)

Transcript & Mutation Effects

hg38 • Region Span ~157.7 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

spermatogenic failure 26LIMITED

Inheritance Pattern: Unknown

Disease ID:MONDO:0054730

Submitter: Labcorp Genetics (formerly Invitae)

Clinical Genomic Database (CGD)

Spermatogenic failure 26AR

Manifestation: Genitourinary

Intervention: General

Rationale: 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

Refs: 28905369

Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to TSGA10 variants in ClinVar

5 Conditions Cataloged

not specifiedTotal: 88

not providedTotal: 11

TSGA10-related disorderTotal: 7

Spermatogenic failure 26Total: 1

Primary ciliary dyskinesiaTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_025244.4. 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	6 clinvar	3 clinvar	11
missense			87 clinvar			87
nonsense						0
start loss						0
frameshift	1 clinvar					1
splice donor/acceptor (+/-2bp)		1 clinvar	3 clinvar	1 clinvar		5
Total	1	1	92	7	3	104

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 90 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_025244.4	RefSeq	NP_079520.1	16	MANE Select
ENST00000393483.8	Ensembl	ENSP00000377123.3	16	MANE Select
NM_001349012.1	RefSeq	NP_001335941.1	16	Standard
NM_001349013.2	RefSeq	NP_001335942.1	13	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

spermatogenesis
cell projection assembly

Molecular Function

molecular_function
protein binding

Cellular Component

cellular_component
centriole
motile cilium
neuron projection

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000393483
Coding exons: 16
Length: 157704
Individuals with no LoFs: 125667
Homozygous LoFs: 0
Heterozygous LoFs: 78
Defined: 125745
p: 0.000310

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.751	330	371	0.890	0.0000196	4638
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000068	0.000062	rare
Latino/Admixed American	0.00024	0.00023	rare
Ashkenazi Jewish	0.00022	0.00020	rare
East Asian	0.00018	0.00016	rare
Finnish	0.00011	0.000092	rare
European (Non-Finnish)	0.00047	0.00046	rare
South Asian	0.00027	0.00026	rare
Other	0.00035	0.00033	rare

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.932

Gene Damage Prediction

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