TSNAXIP1

protein-coding

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

Gene summary

Predicted to be involved in cell differentiation and spermatogenesis. Predicted to be located in perinuclear region of cytoplasm. Predicted to be active in cytoplasm. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_001288990.3

Inheritance

—

ClinVar variants

U:118B:8

Top phenotype

Prostate cancer

gnomAD constraint

pLI —, LoF o/e 1.16

Max pathogenic AF

—

Genomic locus

chr16:67,806,765-67,832,148

External References & Databases

Ensembl (ENSG00000102904)

Transcript & Mutation Effects

hg38 • Region Span ~25.4 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to TSNAXIP1 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 119

Prostate cancerTotal: 1

Primary ciliary dyskinesiaTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001288990.3. 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				1 clinvar		1
missense			115 clinvar	7 clinvar		122
nonsense			2 clinvar			2
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	118	8	0	126

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 52 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001288990.3	RefSeq	NP_001275919.1	16	MANE Select
ENST00000561639.6	Ensembl	ENSP00000457241.1	16	MANE Select
NM_001288991.3	RefSeq	NP_001275920.1	14	Standard
NM_001288992.3	RefSeq	NP_001275921.1	8	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

multicellular organism development
spermatogenesis
biological_process
cell differentiation

Molecular Function

molecular_function

Cellular Component

cellular_component
perinuclear region of cytoplasm

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000388833
Coding exons: 14
Length: 25384
Individuals with no LoFs: 124393
Homozygous LoFs: 2
Heterozygous LoFs: 1353
Defined: 125748
p: 0.00540

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.468	400	375	1.07	0.0000222	4364
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.011	0.0088	notable
Latino/Admixed American	0.0077	0.0072	notable
Ashkenazi Jewish	0.0019	0.0019	notable
East Asian	0.0055	0.0051	notable
Finnish	0.0041	0.0038	notable
European (Non-Finnish)	0.0063	0.0060	notable
South Asian	0.0024	0.0023	notable
Other	0.0037	0.0036	notable

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.464

Gene Damage Prediction

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