SPATA31A1

SPATA31 subfamily A member 1

Basic information

Region (hg38): 9:39355669-39361962

Previous symbols: [ "C9orf36", "FAM75A1", "SPATA31A2", "FAM75A2" ]

Links

ENSG00000204849 ∙ NCBI:647060 ∙ ∙ HGNC:23394 ∙ Uniprot:Q5TZJ5 ∙ 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 SPATA31A1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SPATA31A1 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			70	17		87
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	70	18	0

Variants in SPATA31A1

This is a list of pathogenic ClinVar variants found in the SPATA31A1 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-39355762-T-G		not specified	Uncertain significance (Dec 14, 2024)
9-39355768-C-T		not specified	Uncertain significance (Jan 04, 2022)
9-39355774-C-T		not specified	Uncertain significance (Aug 20, 2024)
9-39355786-C-A		not specified	Uncertain significance (Apr 19, 2024)
9-39355823-T-C			Likely benign (Mar 01, 2025)
9-39357772-C-T		not specified	Uncertain significance (Jun 18, 2021)
9-39357784-C-G		not specified	Likely benign (Dec 07, 2021)
9-39357794-C-T		not specified	Uncertain significance (Jun 18, 2021)
9-39358197-T-G		not specified	Uncertain significance (Mar 29, 2023)
9-39358217-C-T		not specified	Likely benign (Sep 16, 2021)
9-39358229-C-G		not specified	Uncertain significance (Dec 21, 2022)
9-39358229-C-T		not specified	Uncertain significance (Dec 09, 2024)
9-39358246-C-A		not specified	Uncertain significance (Sep 09, 2024)
9-39358246-C-T		not specified	Uncertain significance (Aug 09, 2021)
9-39358247-A-G		not specified	Uncertain significance (Feb 12, 2025)
9-39358249-C-T		not specified	Uncertain significance (Aug 02, 2021)
9-39358273-T-A		not specified	Uncertain significance (Sep 30, 2024)
9-39358303-T-C		not specified	Uncertain significance (Jun 12, 2023)
9-39358310-G-A		not specified	Uncertain significance (Nov 21, 2022)
9-39358360-G-A		not specified	Uncertain significance (Jun 26, 2024)
9-39358373-T-A		not specified	Uncertain significance (Dec 28, 2024)
9-39358375-T-C		not specified	Uncertain significance (Jan 20, 2023)
9-39358403-C-T		not specified	Uncertain significance (Feb 08, 2025)
9-39358454-G-A		not specified	Uncertain significance (Feb 03, 2022)
9-39358549-G-A		not specified	Uncertain significance (Nov 12, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SPATA31A1	protein_coding	protein_coding	ENST00000377647	4	6258

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.378	0.488	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.656	62	49.1	1.26	0.00000242	8693
Missense in Polyphen		6	10.222	0.58698		2196
Synonymous	0.385	17	19.1	0.888	0.00000102	2761
Loss of Function	0.862	0	0.866	0.00	3.62e-8	70

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
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: 0.145
• hipred: N
• hipred_score: 0.139

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Spata31

Gene ontology

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