SPATA6L

spermatogenesis associated 6 like

Basic information

Region (hg38): 9:4553386-4666674

Previous symbols: [ "C9orf68" ]

Links

ENSG00000106686 ∙ NCBI:55064 ∙ ∙ HGNC:25472 ∙ Uniprot:Q8N4H0 ∙ 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 SPATA6L gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SPATA6L 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			31	1		32
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			18	5	4	27
Total	0	0	49	7	4

Variants in SPATA6L

This is a list of pathogenic ClinVar variants found in the SPATA6L region.

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

Position	Type	Phenotype	Significance	ClinVar
9-4561374-C-T			Benign (Nov 12, 2018)
9-4561421-T-C			Benign (Nov 12, 2018)
9-4561426-T-C			Benign (May 16, 2021)
9-4561477-C-T		Dicarboxylic aminoaciduria	Benign (Dec 31, 2019)
9-4561478-G-A		Dicarboxylic aminoaciduria • not specified	Uncertain significance (Aug 10, 2021)
9-4561485-T-C		not specified	Uncertain significance (Jul 16, 2015)
9-4561490-C-A		Dicarboxylic aminoaciduria	Uncertain significance (Jan 12, 2018)
9-4561526-A-G		not specified	Uncertain significance (Sep 28, 2021)
9-4561527-T-C		Dicarboxylic aminoaciduria	Conflicting classifications of pathogenicity (Jun 01, 2024)
9-4561596-G-A			Benign (Nov 12, 2018)
9-4561630-G-A			Benign (May 14, 2021)
9-4561651-G-A			Benign (Nov 12, 2018)
9-4561769-T-C			Benign (Nov 12, 2018)
9-4564404-G-A		not specified	Uncertain significance (Oct 26, 2022)
9-4564411-C-A			Likely benign (Jul 05, 2018)
9-4564416-C-A		Dicarboxylic aminoaciduria	Uncertain significance (Jan 13, 2018)
9-4564428-G-A		not specified	Uncertain significance (Jun 13, 2024)
9-4564432-G-A		Dicarboxylic aminoaciduria	Benign (Jul 15, 2021)
9-4564454-A-C		not specified	Uncertain significance (Aug 02, 2022)
9-4565834-A-G			Benign (May 22, 2021)
9-4566036-G-A		Dicarboxylic aminoaciduria	Benign (May 05, 2021)
9-4566042-A-C		Dicarboxylic aminoaciduria	Uncertain significance (Jan 13, 2018)
9-4566047-G-A		not specified	Likely benign (Feb 05, 2024)
9-4566078-T-C		not specified	Uncertain significance (Feb 06, 2023)
9-4566078-T-G		Dicarboxylic aminoaciduria	Uncertain significance (Jan 13, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SPATA6L	protein_coding	protein_coding	ENST00000475086	9	113289

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.04e-16	0.00139	124742	0	52	124794	0.000208

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-2.46	265	174	1.53	0.00000835	2184
Missense in Polyphen		124	82.675	1.4999		1109
Synonymous	-0.696	72	64.9	1.11	0.00000323	627
Loss of Function	-0.932	22	17.8	1.24	8.43e-7	233

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00188	0.00188
Ashkenazi Jewish	0.00	0.00
East Asian	0.000280	0.000278
Finnish	0.0000947	0.0000928
European (Non-Finnish)	0.0000975	0.0000971
Middle Eastern	0.000280	0.000278
South Asian	0.0000667	0.0000654
Other	0.000165	0.000165

dbNSFP

Source: dbNSFP

Intolerance Scores

• rvis_EVS: 1.22
• rvis_percentile_EVS: 93.21

Haploinsufficiency Scores

• pHI: 0.0765
• hipred: N
• hipred_score: 0.112
• ghis: 0.470

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: 4430402I18Rik