SHTN1

shootin 1

Basic information

Region (hg38): 10:116881477-117126586

Previous symbols: [ "KIAA1598" ]

Links

ENSG00000187164NCBI:57698OMIM:611171HGNC:29319Uniprot:A0MZ66AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SHTN1 gene.

  • not_specified (42 variants)
  • not_provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SHTN1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001127211.3. Only rare variants are included in the table.

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.

EffectPLPVUSLBBSum
synonymous
1
clinvar
1
missense
39
clinvar
3
clinvar
42
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
0
Total 0 0 39 3 1
Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
SHTN1protein_codingprotein_codingENST00000355371 17242356
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.03860.9611257320161257480.0000636
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense2.142093160.6610.00001584162
Missense in Polyphen4495.4870.460791347
Synonymous0.03321131130.9960.000006441110
Loss of Function4.121037.00.2700.00000200469

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0001210.000120
Ashkenazi Jewish0.000.00
East Asian0.00005450.0000544
Finnish0.0001420.000139
European (Non-Finnish)0.00008350.0000791
Middle Eastern0.00005450.0000544
South Asian0.000.00
Other0.000.00

dbNSFP

Source: dbNSFP

Function
FUNCTION: Involved in the generation of internal asymmetric signals required for neuronal polarization and neurite outgrowth. Mediates netrin-1-induced F-actin-substrate coupling or 'clutch engagement' within the axon growth cone through activation of CDC42, RAC1 and PAK1-dependent signaling pathway, thereby converting the F-actin retrograde flow into traction forces, concomitantly with filopodium extension and axon outgrowth. Plays a role in cytoskeletal organization by regulating the subcellular localization of phosphoinositide 3-kinase (PI3K) activity at the axonal growth cone. Plays also a role in regenerative neurite outgrowth. In the developing cortex, cooperates with KIF20B to promote both the transition from the multipolar to the bipolar stage and the radial migration of cortical neurons from the ventricular zone toward the superficial layer of the neocortex. Involved in the accumulation of phosphatidylinositol 3,4,5- trisphosphate (PIP3) in the growth cone of primary hippocampal neurons. {ECO:0000250|UniProtKB:A0MZ67, ECO:0000250|UniProtKB:Q8K2Q9}.;
Pathway
Developmental Biology;Recycling pathway of L1;L1CAM interactions;Axon guidance (Consensus)

Recessive Scores

pRec
0.0868

Intolerance Scores

loftool
rvis_EVS
-0.45
rvis_percentile_EVS
24

Haploinsufficiency Scores

pHI
0.141
hipred
Y
hipred_score
0.688
ghis
0.575

Essentials

essential_gene_CRISPR
essential_gene_CRISPR2
essential_gene_gene_trap
N
gene_indispensability_pred
gene_indispensability_score

Mouse Genome Informatics

Gene name
Shtn1
Phenotype

Gene ontology

Biological process
substrate-dependent cell migration, cell extension;Ras protein signal transduction;axonogenesis;Cdc42 protein signal transduction;netrin-activated signaling pathway;positive regulation of axon extension;neuron projection morphogenesis;cytoplasmic actin-based contraction involved in cell motility;endoplasmic reticulum polarization;actin filament bundle retrograde transport;regulation of establishment of cell polarity;positive regulation of neuron migration
Cellular component
cytoplasm;microtubule;microtubule associated complex;microtubule cytoskeleton;lamellipodium;filopodium;axon;growth cone;cell leading edge;perikaryon;axonal growth cone;perinuclear region of cytoplasm
Molecular function
protein binding;kinesin binding;cadherin binding;actin filament binding