SPATA6

spermatogenesis associated 6

Basic information

Region (hg38): 1:48295372-48472208

Links

ENSG00000132122 ∙ NCBI:54558 ∙ OMIM:613947 ∙ HGNC:18309 ∙ Uniprot:Q9NWH7 ∙ 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 SPATA6 gene.

• Inborn genetic diseases (24 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SPATA6 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
missense			24			24
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	24	0	1

Variants in SPATA6

This is a list of pathogenic ClinVar variants found in the SPATA6 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-48298760-A-T		not specified	Uncertain significance (Jan 24, 2023)
1-48298778-T-C		not specified	Uncertain significance (Nov 10, 2022)
1-48298804-C-T		not specified	Uncertain significance (Jun 30, 2023)
1-48305824-A-C		not specified	Uncertain significance (Jun 24, 2022)
1-48305830-G-C		not specified	Uncertain significance (Jun 21, 2023)
1-48305839-T-C		not specified	Uncertain significance (Dec 27, 2022)
1-48359625-G-A		not specified	Uncertain significance (Feb 21, 2024)
1-48359748-C-T		not specified	Uncertain significance (Mar 21, 2023)
1-48359758-G-T		not specified	Uncertain significance (Aug 04, 2023)
1-48359765-G-C		not specified	Uncertain significance (Aug 02, 2022)
1-48385338-G-A		not specified	Uncertain significance (Dec 14, 2021)
1-48395332-G-T		not specified	Uncertain significance (Jun 02, 2023)
1-48395344-G-T		not specified	Uncertain significance (Nov 15, 2021)
1-48399425-G-A		not specified	Uncertain significance (Feb 09, 2022)
1-48399454-A-G		not specified	Uncertain significance (Jul 20, 2021)
1-48399521-T-C		not specified	Uncertain significance (Dec 07, 2021)
1-48403821-G-A		not specified	Uncertain significance (Nov 08, 2021)
1-48411495-T-G		not specified	Uncertain significance (Dec 07, 2021)
1-48411499-G-A		not specified	Uncertain significance (Sep 06, 2022)
1-48411537-G-A		not specified	Uncertain significance (Oct 12, 2022)
1-48411570-G-A		not specified	Uncertain significance (Jan 23, 2023)
1-48413132-C-T			Benign (Jul 16, 2018)
1-48451594-G-C		not specified	Uncertain significance (Dec 06, 2022)
1-48453026-G-C		not specified	Uncertain significance (Dec 17, 2023)
1-48453092-T-C		not specified	Uncertain significance (Apr 25, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SPATA6	protein_coding	protein_coding	ENST00000371847	13	176802

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.42e-21	0.000599	125661	1	86	125748	0.000346

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.199	251	260	0.965	0.0000137	3167
Missense in Polyphen		153	153.59	0.99618		1899
Synonymous	1.15	83	97.5	0.851	0.00000539	900
Loss of Function	-0.411	30	27.7	1.08	0.00000149	360

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00102	0.00101
Ashkenazi Jewish	0.00	0.00
East Asian	0.000438	0.000435
Finnish	0.00	0.00
European (Non-Finnish)	0.000329	0.000325
Middle Eastern	0.000438	0.000435
South Asian	0.000368	0.000327
Other	0.000535	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Required for formation of the sperm connecting piece during spermiogenesis. Sperm connecting piece is essential for linking the developing flagellum to the head during late spermiogenesis. May be involved in myosin-based microfilament transport through interaction with myosin subunits. {ECO:0000250|UniProtKB:Q3U6K5}.

Recessive Scores

• pRec: 0.104

Intolerance Scores

• loftool: 0.962
• rvis_EVS: -0.31
• rvis_percentile_EVS: 32.15

Haploinsufficiency Scores

• pHI: 0.277
• hipred: N
• hipred_score: 0.227
• ghis: 0.516

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.240

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Spata6
• Phenotype: reproductive system phenotype; limbs/digits/tail phenotype; skeleton phenotype; endocrine/exocrine gland phenotype; cellular phenotype

Gene ontology

• Biological process: multicellular organism development;spermatogenesis;cell differentiation;motile cilium assembly
• Cellular component: extracellular region;sperm connecting piece
• Molecular function: myosin light chain binding