SPAG16

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

Basic information

Region (hg38): 2:213284389-214410501

Links

ENSG00000144451 ∙ NCBI:79582 ∙ OMIM:612173 ∙ HGNC:23225 ∙ Uniprot:Q8N0X2 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Transcripts

Transcript IDs starting with ENST are treated as Ensembl, all others as RefSeq. Showing 4 of 32.

Transcript ID	Protein ID	Coding exons	MANE Select	MANE Plus Clinical
ENST00000331683.10	ENSP00000332592.5	16	yes	-
ENST00000406979.6	ENSP00000385496.2	3	-	-
ENST00000413312.5	ENSP00000390494.1	7	-	-
ENST00000420497.6	ENSP00000411077.1	3	-	-

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SPAG16 gene.

• not_specified (103 variants)
• not_provided (3 variants)
• Fetal_akinesia_deformation_sequence_1 (2 variants)
• Arthrogryposis_multiplex_congenita (2 variants)
• SPAG16-related_disorder (1 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. These statistics are base on transcript: NM_000024532.5. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			2			2
missense			97	7	2	106
nonsense						0
start loss						0
frameshift			1			1
splice donor/acceptor (+/-2bp)			1			1
Total	0	0	101	7	2

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
		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

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

Gene ontology

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