SPATA13

spermatogenesis associated 13, the group of Pleckstrin homology domain containing|MicroRNA protein coding host genes|Dbl family Rho GEFs

Basic information

Region (hg38): 13:23979804-24307074

Links

ENSG00000182957 ∙ NCBI:221178 ∙ OMIM:613324 ∙ HGNC:23222 ∙ Uniprot:Q96N96 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• primary angle-closure glaucoma (Limited), mode of inheritance: AD

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SPATA13 gene.

• Inborn genetic diseases (56 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SPATA13 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			52	4		56
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	52	5	0

Variants in SPATA13

This is a list of pathogenic ClinVar variants found in the SPATA13 region.

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

Position	Type	Phenotype	Significance	ClinVar
13-24222869-C-T		SPATA13-related disorder	Benign (Aug 22, 2019)
13-24222937-A-G		not specified	Uncertain significance (Dec 05, 2022)
13-24222945-G-A		not specified	Uncertain significance (May 03, 2023)
13-24222949-G-A		not specified	Uncertain significance (Jan 19, 2022)
13-24222973-A-G		not specified	Uncertain significance (Jun 24, 2022)
13-24222973-A-T		not specified	Uncertain significance (May 09, 2023)
13-24222999-G-A		not specified	Uncertain significance (Dec 01, 2022)
13-24223015-C-T		not specified	Uncertain significance (Aug 13, 2021)
13-24223031-G-A		SPATA13-related disorder	Likely benign (Feb 22, 2019)
13-24223053-G-A		not specified	Uncertain significance (Aug 09, 2021)
13-24223062-C-T		not specified	Uncertain significance (Sep 17, 2021)
13-24223080-G-A		not specified	Uncertain significance (Jun 06, 2023)
13-24223103-C-T		SPATA13-related disorder	Likely benign (May 24, 2019)
13-24223120-A-T		not specified	Uncertain significance (Oct 26, 2021)
13-24223147-T-C		not specified	Uncertain significance (Sep 07, 2022)
13-24223195-G-C		SPATA13-related disorder	Benign (Aug 12, 2019)
13-24223312-G-A		not specified	Uncertain significance (Mar 07, 2024)
13-24223324-A-T		not specified	Uncertain significance (Sep 07, 2022)
13-24223347-T-G		not specified	Uncertain significance (Oct 26, 2021)
13-24223348-C-T		not specified	Likely benign (Jul 28, 2021)
13-24223425-C-G		not specified	Uncertain significance (May 11, 2022)
13-24223426-C-T		SPATA13-related disorder	Likely benign (Oct 10, 2022)
13-24223429-G-T		not specified	Uncertain significance (Oct 05, 2023)
13-24223452-C-T		not specified	Uncertain significance (Sep 16, 2021)
13-24223508-C-A		not specified	Uncertain significance (Mar 01, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SPATA13	protein_coding	protein_coding	ENST00000424834	12	327269

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00264	0.997	125720	0	28	125748	0.000111

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.03	636	797	0.798	0.0000500	8391
Missense in Polyphen		147	248.91	0.59057		2629
Synonymous	1.78	288	329	0.875	0.0000217	2551
Loss of Function	4.50	14	47.4	0.295	0.00000235	552

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000615	0.0000615
Ashkenazi Jewish	0.000298	0.000298
East Asian	0.0000544	0.0000544
Finnish	0.000140	0.000139
European (Non-Finnish)	0.000162	0.000158
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000327	0.0000327
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Acts as guanine nucleotide exchange factor (GEF) for RHOA, RAC1 and CDC42 GTPases. Regulates cell migration and adhesion assembly and disassembly through a RAC1, PI3K, RHOA and AKT1-dependent mechanism. Increases both RAC1 and CDC42 activity, but decreases the amount of active RHOA. Required for MMP9 up- regulation via the JNK signaling pathway in colorectal tumor cells. Involved in tumor angiogenesis and may play a role in intestinal adenoma formation and tumor progression. {ECO:0000269|PubMed:17145773, ECO:0000269|PubMed:17599059, ECO:0000269|PubMed:19151759, ECO:0000269|PubMed:19893577, ECO:0000269|PubMed:19934221}.
• Pathway: Regulation of actin cytoskeleton - Homo sapiens (human);Regulation of RAC1 activity;Regulation of CDC42 activity (Consensus)

Recessive Scores

• pRec: 0.112

Intolerance Scores

• loftool: 0.257
• rvis_EVS: 2.01
• rvis_percentile_EVS: 97.67

Haploinsufficiency Scores

• pHI: 0.287
• hipred: N
• hipred_score: 0.259

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.214

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Spata13
• Phenotype: homeostasis/metabolism phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); neoplasm; digestive/alimentary phenotype

Gene ontology

• Biological process: cell migration;lamellipodium assembly;regulation of cell migration;regulation of Rho protein signal transduction;filopodium assembly
• Cellular component: nucleoplasm;cytoplasm;cytosol;lamellipodium;filopodium;ruffle membrane
• Molecular function: guanyl-nucleotide exchange factor activity;protein binding;Rac guanyl-nucleotide exchange factor activity