SPAG16

sperm associated antigen 16, the group of WD repeat domain containing|MicroRNA protein coding host genes

Basic information

Region (hg38): 2:213284388-214410501

Links

ENSG00000144451 ∙ NCBI:79582 ∙ OMIM:612173 ∙ HGNC:23225 ∙ Uniprot:Q8N0X2 ∙ 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 SPAG16 gene.

• Inborn genetic diseases (23 variants)
• Arthrogryposis multiplex congenita;Fetal akinesia deformation sequence 1 (2 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SPAG16 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			23		1	24
nonsense						0
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	24	0	1

Variants in SPAG16

This is a list of pathogenic ClinVar variants found in the SPAG16 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-213284548-G-T		not specified	Uncertain significance (Oct 25, 2022)
2-213284560-C-T		not specified	Uncertain significance (Mar 01, 2023)
2-213296097-A-G		not specified	Uncertain significance (Aug 17, 2022)
2-213296103-A-G		not specified	Uncertain significance (Dec 13, 2023)
2-213297265-C-A		not specified	Uncertain significance (Sep 01, 2021)
2-213297278-T-A		not specified	Uncertain significance (Nov 20, 2023)
2-213310062-C-T		not specified	Uncertain significance (Dec 20, 2021)
2-213310074-C-T		not specified	Uncertain significance (Apr 26, 2023)
2-213317226-T-A		not specified	Uncertain significance (Mar 07, 2023)
2-213317300-G-C		not specified	Uncertain significance (Aug 12, 2022)
2-213340200-C-T		not specified	Uncertain significance (Nov 15, 2021)
2-213350524-A-G		SPAG16-related disorder	Likely benign (Feb 01, 2021)
2-213350587-A-G		not specified	Uncertain significance (Dec 14, 2023)
2-213350614-C-T		not specified	Uncertain significance (Feb 16, 2023)
2-213375022-G-A		not specified	Uncertain significance (Sep 17, 2021)
2-213375037-C-T		not specified	Uncertain significance (Jul 25, 2023)
2-213375066-C-T		not specified	Uncertain significance (Dec 03, 2021)
2-213375067-G-A		not specified	Uncertain significance (Dec 13, 2021)
2-213489976-C-T		not specified	Uncertain significance (Jun 03, 2022)
2-213489990-C-A			Benign (Aug 15, 2017)
2-213490018-A-G		not specified	Uncertain significance (Oct 04, 2022)
2-213862481-G-T			Benign (Aug 15, 2017)
2-213862517-T-A		not specified	Uncertain significance (Apr 25, 2023)
2-213862535-G-A		not specified	Uncertain significance (Jan 03, 2024)
2-213930054-C-T		not specified	Uncertain significance (Mar 01, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SPAG16	protein_coding	protein_coding	ENST00000331683	16	1126113

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.40e-34	1.44e-7	125153	0	595	125748	0.00237

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.869	374	330	1.13	0.0000164	4161
Missense in Polyphen		100	92.124	1.0855		1181
Synonymous	-0.669	128	119	1.08	0.00000626	1148
Loss of Function	-1.81	45	33.7	1.34	0.00000171	424

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00163	0.00161
Ashkenazi Jewish	0.00221	0.00218
East Asian	0.000164	0.000163
Finnish	0.000791	0.000786
European (Non-Finnish)	0.00385	0.00381
Middle Eastern	0.000164	0.000163
South Asian	0.00224	0.00222
Other	0.00266	0.00261

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Necessary for sperm flagellar function. Plays a role in motile ciliogenesis. May help to recruit STK36 to the cilium or apical surface of the cell to initiate subsequent steps of construction of the central pair apparatus of motile cilia (By similarity). {ECO:0000250}.

Recessive Scores

• pRec: 0.109

Intolerance Scores

• loftool: 0.541
• rvis_EVS: 0.18
• rvis_percentile_EVS: 66.13

Haploinsufficiency Scores

• pHI: 0.0791
• hipred: N
• hipred_score: 0.146
• ghis: 0.516

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.417

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Spag16
• Phenotype: cellular phenotype; endocrine/exocrine gland phenotype; reproductive system phenotype

Gene ontology

• Biological process: sperm axoneme assembly;axoneme assembly;cilium assembly
• Cellular component: axoneme;sperm flagellum;axonemal central apparatus