SPATA31D1

SPATA31 subfamily D member 1

Basic information

Region (hg38): 9:81988772-81995253

Previous symbols: [ "FAM75D1" ]

Links

ENSG00000214929 ∙ NCBI:389763 ∙ ∙ HGNC:37283 ∙ Uniprot:Q6ZQQ2 ∙ 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 SPATA31D1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SPATA31D1 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				2	1	3
missense			207	16	1	224
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	207	18	2

Variants in SPATA31D1

This is a list of pathogenic ClinVar variants found in the SPATA31D1 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-81988831-C-T		not specified	Uncertain significance (Sep 01, 2021)
9-81988834-T-C		not specified	Uncertain significance (Sep 29, 2023)
9-81988845-C-G		not specified	Uncertain significance (Oct 29, 2024)
9-81988852-A-G		not specified	Uncertain significance (Mar 04, 2025)
9-81988859-C-G		not specified	Uncertain significance (Mar 07, 2024)
9-81988884-G-T		not specified	Likely benign (Jun 29, 2023)
9-81988951-G-A		not specified	Uncertain significance (Jun 23, 2023)
9-81988961-C-T		not specified	Uncertain significance (Nov 08, 2022)
9-81988970-C-T		not specified	Likely benign (Sep 26, 2022)
9-81989808-G-T		not specified	Uncertain significance (Nov 10, 2024)
9-81990435-G-C		not specified	Uncertain significance (Nov 23, 2024)
9-81990485-A-G		not specified	Uncertain significance (Feb 05, 2024)
9-81990777-G-A		not specified	Uncertain significance (Jun 16, 2022)
9-81990781-C-T		not specified	Uncertain significance (Feb 26, 2024)
9-81990789-T-A		not specified	Uncertain significance (Oct 20, 2023)
9-81990790-C-T		not specified	Uncertain significance (Oct 20, 2023)
9-81990793-G-T		not specified	Uncertain significance (Nov 10, 2024)
9-81990801-C-T		not specified	Uncertain significance (May 31, 2023)
9-81990808-A-G		not specified	Uncertain significance (Feb 06, 2025)
9-81990826-A-T		not specified	Uncertain significance (Jan 03, 2024)
9-81990827-C-A		not specified	Uncertain significance (Dec 19, 2023)
9-81990843-T-C		not specified	Uncertain significance (Apr 19, 2024)
9-81990872-G-C		not specified	Likely benign (Aug 04, 2023)
9-81990892-A-G		not specified	Uncertain significance (Dec 05, 2024)
9-81990928-C-T		not specified	Uncertain significance (Oct 22, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SPATA31D1	protein_coding	protein_coding	ENST00000344803	4	6485

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00382	0.656	120068	0	3	120071	0.0000125

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-5.27	1227	806	1.52	0.0000430	10242
Missense in Polyphen		189	140.96	1.3408		2169
Synonymous	-5.49	443	318	1.39	0.0000173	3208
Loss of Function	0.567	4	5.43	0.737	2.28e-7	70

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000621	0.0000621
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	0.0000356	0.0000344
Other	0.00	0.00

dbNSFP

Source: dbNSFP

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

Intolerance Scores

• rvis_EVS: 0.57
• rvis_percentile_EVS: 81.74

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.158
• ghis: 0.419

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: 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: Spata31d1d

Gene ontology

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