SPAG17

sperm associated antigen 17

Basic information

Region (hg38): 1:117953590-118185228

Links

ENSG00000155761 ∙ NCBI:200162 ∙ OMIM:616554 ∙ HGNC:26620 ∙ Uniprot:Q6Q759 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• male infertility with azoospermia or oligozoospermia due to single gene mutation (Moderate), mode of inheritance: AR
• non-syndromic male infertility due to sperm motility disorder (Supportive), mode of inheritance: AR
• spermatogenic failure 55 (Limited), mode of inheritance: Unknown

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Spermatogenic failure 55	AR	General	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	Genitourinary	28548327

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SPAG17 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SPAG17 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	14	10	25
missense		1	119	18	11	149
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				4	3	7
non coding			10	2	1	13
Total	0	1	130	34	22

Variants in SPAG17

This is a list of pathogenic ClinVar variants found in the SPAG17 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-117954595-A-G		not specified	Uncertain significance (Mar 25, 2024)
1-117955349-T-G		not specified	Uncertain significance (Jul 06, 2024)
1-117957091-T-C		not specified	Uncertain significance (Jul 30, 2023)
1-117957101-C-G		not specified	Uncertain significance (Dec 02, 2024)
1-117957157-A-T		not specified	Uncertain significance (Oct 09, 2024)
1-117957178-G-T		not specified	Uncertain significance (Apr 01, 2024)
1-117958938-C-A		not specified	Uncertain significance (May 25, 2022)
1-117958941-A-G		not specified	Uncertain significance (Dec 19, 2022)
1-117958941-A-T		not specified	Uncertain significance (Aug 08, 2023)
1-117958953-G-A		not specified	Uncertain significance (Sep 29, 2022)
1-117958969-G-A		not specified	Likely benign (Mar 18, 2024)
1-117958978-C-T		not specified	Uncertain significance (Aug 12, 2024)
1-117958997-A-C		not specified	Uncertain significance (Dec 19, 2022)
1-117959002-G-A		not specified	Uncertain significance (Apr 01, 2024)
1-117959306-C-A		not specified	Uncertain significance (Oct 05, 2023)
1-117959343-G-A		not specified	Uncertain significance (Apr 22, 2022)
1-117959352-A-G		not specified	Uncertain significance (Jan 02, 2024)
1-117959353-G-A		not specified	Uncertain significance (Feb 12, 2024)
1-117959358-G-C		not specified	Uncertain significance (Mar 31, 2024)
1-117963816-T-G		not specified	Uncertain significance (Feb 15, 2023)
1-117963818-C-T		SPAG17-related disorder	Likely benign (Apr 01, 2019)
1-117963819-G-A		not specified	Uncertain significance (Aug 15, 2023)
1-117963852-T-C		not specified	Uncertain significance (Feb 14, 2023)
1-117963898-G-T		not specified	Uncertain significance (Oct 06, 2023)
1-117966611-G-C		not specified	Uncertain significance (Apr 11, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SPAG17	protein_coding	protein_coding	ENST00000336338	48	231363

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.19e-24	1.00	125509	1	238	125748	0.000951

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0798	1126	1.13e+3	0.993	0.0000561	14678
Missense in Polyphen		349	378.69	0.9216		5116
Synonymous	0.250	381	387	0.984	0.0000194	4041
Loss of Function	5.00	60	119	0.505	0.00000585	1545

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00398	0.00396
Ashkenazi Jewish	0.000199	0.000198
East Asian	0.000588	0.000544
Finnish	0.000232	0.000231
European (Non-Finnish)	0.000713	0.000677
Middle Eastern	0.000588	0.000544
South Asian	0.00216	0.00157
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Component of the central pair apparatus of ciliary axonemes. Plays a critical role in the function and structure of motile cilia. May play a role in endochondral bone formation, most likely because of a function in primary cilia of chondrocytes and osteoblasts. {ECO:0000250|UniProtKB:Q5S003}.

Intolerance Scores

• loftool: 0.981
• rvis_EVS: 0.6
• rvis_percentile_EVS: 82.88

Haploinsufficiency Scores

• pHI: 0.127
• hipred: N
• hipred_score: 0.331
• ghis: 0.445

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.101

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	High	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High

Mouse Genome Informatics

• Gene name: Spag17
• Phenotype: homeostasis/metabolism phenotype; cellular phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); respiratory system phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan)

Gene ontology

• Biological process: epithelial cilium movement;axonemal central apparatus assembly
• Cellular component: microtubule;motile cilium;axonemal central apparatus