SPATA31A6

SPATA31 subfamily A member 6

Basic information

Region (hg38): 9:42183659-42189887

Previous symbols: [ "FAM75A6" ]

Links

ENSG00000185775 ∙ NCBI:389730 ∙ ∙ HGNC:32006 ∙ Uniprot:Q5VVP1 ∙ 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 SPATA31A6 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SPATA31A6 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				4		4
missense			195	26		221
nonsense				1		1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	195	31	0

Variants in SPATA31A6

This is a list of pathogenic ClinVar variants found in the SPATA31A6 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-42183706-C-G		not specified	Uncertain significance (Apr 30, 2024)
9-42183727-T-C		not specified	Uncertain significance (Jan 09, 2025)
9-42183738-C-T			Likely benign (Jul 01, 2022)
9-42183749-C-T		not specified	Uncertain significance (Dec 13, 2021)
9-42183755-C-A		not specified	Uncertain significance (Oct 27, 2022)
9-42183778-A-T		not specified	Uncertain significance (Jan 16, 2025)
9-42183779-C-T		not specified	Uncertain significance (Jul 07, 2024)
9-42183797-G-T		not specified	Uncertain significance (Feb 12, 2025)
9-42183804-C-A		not specified	Uncertain significance (Aug 12, 2021)
9-42183814-C-T		not specified	Likely benign (Mar 20, 2024)
9-42183826-T-G		not specified	Uncertain significance (Mar 07, 2023)
9-42183854-C-T		not specified	Likely benign (Jun 07, 2024)
9-42183860-C-T		not specified	Uncertain significance (Nov 26, 2024)
9-42185073-C-T		not specified	Uncertain significance (Dec 19, 2023)
9-42185081-C-T		not specified	Uncertain significance (Feb 04, 2025)
9-42185087-C-T		not specified	Uncertain significance (May 26, 2022)
9-42185088-G-A		not specified	Uncertain significance (Feb 05, 2024)
9-42185716-G-C		not specified	Uncertain significance (Sep 27, 2024)
9-42185736-C-T		not specified	Uncertain significance (Feb 27, 2023)
9-42186012-C-T		not specified	Uncertain significance (Dec 21, 2023)
9-42186035-A-C		not specified	Uncertain significance (Aug 27, 2024)
9-42186039-G-T		not specified	Uncertain significance (Mar 03, 2025)
9-42186045-G-T		not specified	Uncertain significance (Sep 17, 2021)
9-42186057-G-A		not specified	Uncertain significance (Feb 06, 2023)
9-42186057-G-C		not specified	Uncertain significance (Oct 16, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SPATA31A6	protein_coding	protein_coding	ENST00000332857	4	6224

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000255	0.183	118846	7	13	118866	0.0000841

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-4.59	637	384	1.66	0.0000195	8446
Missense in Polyphen		134	79.196	1.692		1995
Synonymous	-5.99	248	154	1.61	0.00000814	2666
Loss of Function	-0.771	6	4.28	1.40	1.78e-7	67

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000545	0.000457
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.000133	0.000101
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role in spermatogenesis. {ECO:0000250}.

Haploinsufficiency Scores

• pHI: 0.0778
• ghis: 0.415

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Spata31

Gene ontology

• Biological process: spermatogenesis;cell differentiation
• Cellular component: integral component of membrane