SPATA16

spermatogenesis associated 16

Basic information

Region (hg38): 3:172889357-173141235

Links

ENSG00000144962 ∙ NCBI:83893 ∙ OMIM:609856 ∙ HGNC:29935 ∙ Uniprot:Q9BXB7 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• male infertility due to globozoospermia (Supportive), mode of inheritance: AR
• spermatogenic failure 6 (Limited), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Spermatogenic failure 6	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	17847006

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SPATA16 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SPATA16 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			9	2	2	13
missense			38	4	5	47
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)			1			1
splice region						0
non coding			9	1	1	11
Total	0	0	57	7	8

Variants in SPATA16

This is a list of pathogenic ClinVar variants found in the SPATA16 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-172889413-G-A		Globozoospermia	Uncertain significance (Apr 28, 2017)
3-172889432-G-T		Globozoospermia	Uncertain significance (Jan 13, 2018)
3-172889478-T-C		Globozoospermia	Uncertain significance (Jan 13, 2018)
3-172889572-A-G		SPATA16-related disorder	Benign (Dec 31, 2019)
3-172889573-C-G		SPATA16-related disorder	Benign (Dec 31, 2019)
3-172889589-T-C		not specified	Uncertain significance (Nov 29, 2021)
3-172889593-G-T		not specified	Uncertain significance (May 25, 2022)
3-172889667-T-C		not specified	Uncertain significance (May 16, 2023)
3-172889670-A-G		not specified	Uncertain significance (Jun 03, 2024)
3-172889680-C-T		not specified	Uncertain significance (Nov 03, 2022)
3-172889694-T-C		Globozoospermia	Uncertain significance (Oct 10, 2018)
3-172913671-A-G		Globozoospermia	Likely benign (Jan 12, 2018)
3-172913722-G-A		Globozoospermia	Likely benign (Jan 13, 2018)
3-172913735-G-A		Globozoospermia	Uncertain significance (Jan 13, 2018)
3-172916302-A-G		Globozoospermia	Uncertain significance (Jan 13, 2018)
3-172916329-C-G		not specified	Uncertain significance (Jan 23, 2024)
3-172916363-G-A		not specified	Uncertain significance (Jul 21, 2021)
3-172916369-T-G		not specified	Uncertain significance (Apr 27, 2022)
3-172916378-G-A		not specified	Uncertain significance (Sep 10, 2024)
3-172916419-C-A		Globozoospermia	Uncertain significance (Jan 13, 2018)
3-172916426-A-T		not specified	Uncertain significance (Nov 21, 2024)
3-172916431-G-T		Globozoospermia	Uncertain significance (Jan 13, 2018)
3-172916455-C-A		Globozoospermia	Likely benign (Jan 13, 2018)
3-172916459-C-T		Globozoospermia	Uncertain significance (Jan 13, 2018)
3-172924222-T-C		Globozoospermia	Uncertain significance (Jan 13, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SPATA16	protein_coding	protein_coding	ENST00000351008	10	251911

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.45e-10	0.571	124719	0	1028	125747	0.00410

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.201	285	295	0.967	0.0000150	3783
Missense in Polyphen		11	12.933	0.85055		152
Synonymous	0.159	94	96.0	0.979	0.00000471	1012
Loss of Function	1.31	19	26.2	0.724	0.00000121	345

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00959	0.00925
Ashkenazi Jewish	0.00200	0.00199
East Asian	0.00750	0.00742
Finnish	0.00281	0.00250
European (Non-Finnish)	0.00504	0.00493
Middle Eastern	0.00750	0.00742
South Asian	0.00183	0.00183
Other	0.00299	0.00294

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in the formation of sperm acrosome, which implicated its potential role in spermatogenesis and sperm-egg fusion. {ECO:0000269|PubMed:12529416}.

Intolerance Scores

• loftool: 0.942
• rvis_EVS: 1.73
• rvis_percentile_EVS: 96.6

Haploinsufficiency Scores

• pHI: 0.162
• hipred: N
• hipred_score: 0.144

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 9.58e-10

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Spata16
• Phenotype: endocrine/exocrine gland phenotype; cellular phenotype; reproductive system phenotype

Gene ontology

• Biological process: multicellular organism development;spermatogenesis;biological_process;cell differentiation
• Cellular component: Golgi apparatus
• Molecular function: molecular_function