SPAG6

sperm associated antigen 6, the group of Armadillo repeat containing|Cilia and flagella associated

Basic information

Region (hg38): 10:22345444-22454224

Links

ENSG00000077327 ∙ NCBI:9576 ∙ OMIM:605730 ∙ HGNC:11215 ∙ Uniprot:O75602 ∙ 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 SPAG6 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SPAG6 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	1	2
missense			20			20
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				1		1
Total	0	0	20	2	1

Variants in SPAG6

This is a list of pathogenic ClinVar variants found in the SPAG6 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-22345802-G-C		not specified	Uncertain significance (Aug 05, 2023)
10-22360822-A-C		SPAG6-related disorder	Likely benign (Sep 29, 2020)
10-22364898-C-G		not specified	Uncertain significance (Feb 16, 2023)
10-22368647-G-C		not specified	Uncertain significance (Jan 18, 2022)
10-22368663-G-A		not specified	Uncertain significance (Apr 01, 2022)
10-22386815-G-A			Benign (Jun 01, 2018)
10-22386838-T-C		not specified	Uncertain significance (Nov 08, 2021)
10-22386849-G-A		not specified	Uncertain significance (Mar 30, 2024)
10-22386862-T-C		not specified	Uncertain significance (May 07, 2024)
10-22386864-G-T		not specified	Likely benign (Mar 30, 2024)
10-22386942-C-A		not specified	Uncertain significance (Nov 09, 2023)
10-22387844-A-T		not specified	Uncertain significance (Oct 07, 2022)
10-22387907-G-C		not specified	Uncertain significance (Sep 21, 2023)
10-22387994-G-A		not specified	Uncertain significance (May 30, 2023)
10-22389220-T-A		not specified	Uncertain significance (Oct 12, 2022)
10-22389235-C-T		not specified	Uncertain significance (Dec 13, 2023)
10-22389236-G-T		not specified	Uncertain significance (Feb 17, 2024)
10-22389265-G-A		not specified	Uncertain significance (Apr 04, 2024)
10-22389289-G-A		not specified	Uncertain significance (Mar 20, 2023)
10-22389305-T-C		not specified	Uncertain significance (Nov 10, 2022)
10-22391758-A-G			Likely benign (Apr 04, 2018)
10-22391764-A-T		not specified	Uncertain significance (Apr 01, 2024)
10-22391886-T-C		not specified	Uncertain significance (Dec 15, 2022)
10-22391903-G-C		not specified	Uncertain significance (Jun 07, 2024)
10-22401173-A-G		not specified	Uncertain significance (Mar 26, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SPAG6	protein_coding	protein_coding	ENST00000376624	11	108755

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.30e-13	0.0891	125678	0	70	125748	0.000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.743	238	273	0.873	0.0000136	3274
Missense in Polyphen		60	75.33	0.7965		986
Synonymous	-0.688	114	105	1.09	0.00000582	1038
Loss of Function	0.674	22	25.7	0.857	0.00000135	305

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000272	0.000272
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.00105	0.00103
Finnish	0.000277	0.000277
European (Non-Finnish)	0.000257	0.000255
Middle Eastern	0.00105	0.00103
South Asian	0.000239	0.000229
Other	0.000329	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Important for structural integrity of the central apparatus in the sperm tail and for flagellar motility. {ECO:0000250, ECO:0000269|PubMed:10493827}.

Recessive Scores

• pRec: 0.107

Intolerance Scores

• loftool: 0.770
• rvis_EVS: -0.03
• rvis_percentile_EVS: 51.66

Haploinsufficiency Scores

• pHI: 0.131
• hipred: N
• hipred_score: 0.454
• ghis: 0.457

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.278

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Spag6

Gene ontology

• Biological process: spermatid development;cell projection organization
• Cellular component: nucleus;microtubule;axoneme;microtubule cytoskeleton;motile cilium