SPATA17

spermatogenesis associated 17, the group of Cilia and flagella associated

Basic information

Region (hg38): 1:217631324-217871696

Links

ENSG00000162814 ∙ NCBI:128153 ∙ OMIM:611032 ∙ HGNC:25184 ∙ Uniprot:Q96L03 ∙ 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 SPATA17 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SPATA17 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			24	3		27
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	24	3	0

Variants in SPATA17

This is a list of pathogenic ClinVar variants found in the SPATA17 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-217631383-C-T		not specified	Uncertain significance (Aug 06, 2021)
1-217631440-G-C		not specified	Uncertain significance (Jan 04, 2024)
1-217648887-T-C		not specified	Uncertain significance (Jan 06, 2023)
1-217648958-C-T		not specified	Uncertain significance (Oct 29, 2024)
1-217648959-G-A		not specified	Uncertain significance (Jul 09, 2024)
1-217648969-C-G		not specified	Uncertain significance (Nov 03, 2022)
1-217648974-A-G			Likely benign (Apr 01, 2023)
1-217669048-A-C		not specified	Uncertain significance (Aug 09, 2021)
1-217669066-A-G		not specified	Uncertain significance (Oct 03, 2022)
1-217669078-G-C		not specified	Uncertain significance (Feb 22, 2025)
1-217683268-G-A		not specified	Uncertain significance (Sep 26, 2023)
1-217683289-G-A		not specified	Uncertain significance (Dec 04, 2024)
1-217683336-G-A		not specified	Uncertain significance (Sep 28, 2022)
1-217742003-A-G		not specified	Uncertain significance (Jan 09, 2024)
1-217742024-G-A		not specified	Uncertain significance (Dec 13, 2022)
1-217742082-T-A		not specified	Uncertain significance (May 27, 2022)
1-217774358-T-C		not specified	Uncertain significance (Nov 10, 2021)
1-217774399-G-T		not specified	Uncertain significance (Aug 02, 2022)
1-217774412-A-G		not specified	Uncertain significance (Aug 08, 2023)
1-217774473-G-T		not specified	Uncertain significance (Jan 22, 2024)
1-217774520-A-G		not specified	Likely benign (Sep 14, 2023)
1-217782175-G-A		not specified	Uncertain significance (Dec 11, 2024)
1-217782190-T-C		not specified	Uncertain significance (Jan 16, 2024)
1-217782210-C-T		not specified	Uncertain significance (Feb 19, 2025)
1-217782238-G-A		not specified	Uncertain significance (Aug 01, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SPATA17	protein_coding	protein_coding	ENST00000366933	10	240373

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.47e-7	0.990	125666	1	81	125748	0.000326

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.787	223	192	1.16	0.0000101	2343
Missense in Polyphen		54	50.601	1.0672		564
Synonymous	0.265	64	66.8	0.959	0.00000329	629
Loss of Function	2.38	16	30.1	0.532	0.00000185	323

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000680	0.000670
Ashkenazi Jewish	0.00	0.00
East Asian	0.000392	0.000381
Finnish	0.0000928	0.0000924
European (Non-Finnish)	0.000215	0.000211
Middle Eastern	0.000392	0.000381
South Asian	0.00120	0.00108
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0882

Intolerance Scores

• rvis_EVS: -0.13
• rvis_percentile_EVS: 43.91

Haploinsufficiency Scores

• pHI: 0.0392
• hipred: N
• hipred_score: 0.492
• ghis: 0.397

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0340

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Spata17

Gene ontology

• Cellular component: cytoplasm
• Molecular function: calmodulin binding