GeneBe

SPATA13

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

Basic information

Region (hg38): 13:23979810-24035027

Links

ENSG00000228741 ∙ 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.

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
10
clinvar
 10
missense
79
clinvar
9
clinvar
6
clinvar
 94
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
2
 2
non coding
2
clinvar
 2
Total 0 0 79 19 8

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
SPATA13protein_codingprotein_codingENST00000424834 12327269
pLI Probability
LOF Intolerant 		pRec Probability
LOF Recessive 		Individuals with
no LOFs 		Individuals with
Homozygous LOFs 		Individuals with
Heterozygous LOFs 		Defined p
0.002640.9971257200281257480.000111
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense2.036367970.7980.00005008391
Missense in Polyphen147248.910.590572629
Synonymous1.782883290.8750.00002172551
Loss of Function4.501447.40.2950.00000235552

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.00006150.0000615
Ashkenazi Jewish0.0002980.000298
East Asian0.00005440.0000544
Finnish0.0001400.000139
European (Non-Finnish)0.0001620.000158
Middle Eastern0.00005440.0000544
South Asian0.00003270.0000327
Other0.0001630.000163

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
ghis

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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