SPATA4

spermatogenesis associated 4, the group of Cilia and flagella associated

Basic information

Region (hg38): 4:176184579-176195585

Links

ENSG00000150628 ∙ NCBI:132851 ∙ OMIM:609879 ∙ HGNC:17333 ∙ Uniprot:Q8NEY3 ∙ 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 SPATA4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SPATA4 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				1		1
missense			25	3		28
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			2			2
Total	0	0	27	4	0

Variants in SPATA4

This is a list of pathogenic ClinVar variants found in the SPATA4 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-176184853-T-C		not specified	Uncertain significance (Apr 22, 2024)
4-176184886-A-G		not specified	Likely benign (Jan 04, 2024)
4-176188141-T-A		not specified	Uncertain significance (Jan 05, 2022)
4-176188153-T-G		not specified	Uncertain significance (Nov 28, 2023)
4-176188161-A-G		not specified	Uncertain significance (Sep 05, 2024)
4-176188166-C-T		not specified	Likely benign (Jul 11, 2023)
4-176188167-G-C		not specified	Uncertain significance (Jan 05, 2022)
4-176188178-T-C		not specified	Uncertain significance (Dec 01, 2022)
4-176188215-T-A		not specified	Uncertain significance (Sep 30, 2021)
4-176188234-T-A		not specified	Uncertain significance (Feb 09, 2023)
4-176192647-A-G		not specified	Uncertain significance (Apr 12, 2024)
4-176192656-T-C		not specified	Uncertain significance (Jun 10, 2024)
4-176192662-A-G		not specified	Uncertain significance (Dec 10, 2024)
4-176192686-G-A		not specified	Likely benign (Nov 01, 2022)
4-176192711-T-C		not specified	Uncertain significance (Dec 14, 2022)
4-176192756-A-T		not specified	Uncertain significance (Sep 11, 2024)
4-176192783-G-T		not specified	Uncertain significance (Jun 10, 2024)
4-176192786-G-A		not specified	Uncertain significance (Feb 05, 2024)
4-176192792-G-A		not specified	Uncertain significance (Jun 05, 2024)
4-176192812-G-A		not specified	Uncertain significance (Oct 06, 2021)
4-176192971-A-T		not specified	Uncertain significance (Feb 28, 2023)
4-176192972-T-A		not specified	Uncertain significance (Mar 05, 2024)
4-176193066-C-A		not specified	Uncertain significance (Apr 04, 2023)
4-176193462-C-T			Likely benign (Feb 01, 2024)
4-176193517-A-G		not specified	Uncertain significance (Dec 15, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SPATA4	protein_coding	protein_coding	ENST00000280191	6	11034

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.18e-9	0.101	125132	2	614	125748	0.00245

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.319	171	160	1.07	0.00000773	1968
Missense in Polyphen		46	42.516	1.082		568
Synonymous	1.22	47	58.9	0.798	0.00000276	585
Loss of Function	0.113	14	14.5	0.968	7.76e-7	176

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00151	0.00150
Ashkenazi Jewish	0.000498	0.000496
East Asian	0.000166	0.000163
Finnish	0.00564	0.00565
European (Non-Finnish)	0.00332	0.00330
Middle Eastern	0.000166	0.000163
South Asian	0.00207	0.00196
Other	0.00230	0.00228

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role in apoptosis regulation. {ECO:0000269|PubMed:26424010}.

Recessive Scores

• pRec: 0.0609

Intolerance Scores

• rvis_EVS: 0.24
• rvis_percentile_EVS: 69.21

Haploinsufficiency Scores

• pHI: 0.0518
• hipred: N
• hipred_score: 0.123

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0392

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Spata4
• Phenotype: normal phenotype

Gene ontology

• Biological process: cilium-dependent cell motility
• Cellular component: cellular_component;nucleus;cytoplasm;motile cilium
• Molecular function: molecular_function;protein binding