SPATA25

spermatogenesis associated 25

Basic information

Region (hg38): 20:45886490-45887622

Previous symbols: [ "C20orf165" ]

Links

ENSG00000149634 ∙ NCBI:128497 ∙ OMIM:618936 ∙ HGNC:16158 ∙ Uniprot:Q9BR10 ∙ 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 SPATA25 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SPATA25 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			10			10
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	10	0	0

Variants in SPATA25

This is a list of pathogenic ClinVar variants found in the SPATA25 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-45886626-T-C		not specified	Uncertain significance (Dec 26, 2023)
20-45886660-C-T		not specified	Uncertain significance (Dec 21, 2021)
20-45886671-A-G		not specified	Uncertain significance (Aug 16, 2022)
20-45886695-A-C		not specified	Uncertain significance (Feb 27, 2024)
20-45886698-G-A		not specified	Uncertain significance (Jul 26, 2021)
20-45886767-T-G		not specified	Uncertain significance (May 29, 2024)
20-45886783-C-G		not specified	Uncertain significance (Apr 08, 2022)
20-45886804-G-A		not specified	Uncertain significance (Apr 09, 2024)
20-45886975-C-T		not specified	Uncertain significance (Jan 30, 2024)
20-45887023-C-A		not specified	Uncertain significance (Mar 29, 2022)
20-45887058-C-A		not specified	Uncertain significance (Jun 22, 2021)
20-45887133-G-A		not specified	Uncertain significance (Jun 29, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SPATA25	protein_coding	protein_coding	ENST00000372519	2	1147

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00146	0.689	125693	0	55	125748	0.000219

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.315	139	129	1.08	0.00000690	1441
Missense in Polyphen		42	37.257	1.1273		411
Synonymous	0.490	51	55.7	0.916	0.00000328	511
Loss of Function	0.739	5	7.13	0.701	3.96e-7	68

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.00	0.00
East Asian	0.000163	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.0000352	0.0000352
Middle Eastern	0.000163	0.000163
South Asian	0.00154	0.00154
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role in spermatogenesis. {ECO:0000269|PubMed:19240080}.

Intolerance Scores

• rvis_EVS: 0.99
• rvis_percentile_EVS: 90.56

Haploinsufficiency Scores

• pHI: 0.520
• hipred: N
• hipred_score: 0.248
• ghis: 0.415

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Spata25
• Phenotype: normal phenotype; skeleton phenotype

Gene ontology

• Biological process: spermatogenesis;cell differentiation
• Cellular component: cellular_component;integral component of membrane
• Molecular function: molecular_function