SHTN1

shootin 1

Basic information

Region (hg38): 10:116881476-117126586

Previous symbols: [ "KIAA1598" ]

Links

ENSG00000187164 ∙ NCBI:57698 ∙ OMIM:611171 ∙ HGNC:29319 ∙ Uniprot:A0MZ66 ∙ 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 SHTN1 gene.

• Inborn genetic diseases (13 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.

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			8	2		10
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			3			3
Total	0	0	11	2	1

Variants in SHTN1

This is a list of pathogenic ClinVar variants found in the SHTN1 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-116881536-T-C		not specified	Uncertain significance (May 03, 2023)
10-116881577-C-T		not specified	Uncertain significance (Nov 01, 2022)
10-116881628-G-C		not specified	Uncertain significance (May 03, 2023)
10-116901771-G-A		not specified	Uncertain significance (Aug 02, 2021)
10-116901805-G-A		not specified	Likely benign (Feb 23, 2023)
10-116901820-G-A		not specified	Uncertain significance (Oct 06, 2021)
10-116901826-G-A		not specified	Uncertain significance (Feb 07, 2023)
10-116906651-C-A		not specified	Uncertain significance (Sep 16, 2021)
10-116906656-C-T		not specified	Uncertain significance (Jan 17, 2024)
10-116906699-G-T		not specified	Likely benign (Apr 13, 2023)
10-116911832-C-T			Benign (Jan 30, 2018)
10-116915404-C-T		not specified	Uncertain significance (Oct 02, 2023)
10-116927829-G-C		not specified	Uncertain significance (Jan 24, 2023)
10-116929855-G-A		not specified	Uncertain significance (Jan 24, 2024)
10-116951926-C-T		not specified	Uncertain significance (Jan 26, 2022)
10-116954089-C-T		not specified	Uncertain significance (Sep 14, 2022)
10-117005070-A-C		not specified	Uncertain significance (Sep 14, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SHTN1	protein_coding	protein_coding	ENST00000355371	17	242356

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0386	0.961	125732	0	16	125748	0.0000636

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.14	209	316	0.661	0.0000158	4162
Missense in Polyphen		44	95.487	0.46079		1347
Synonymous	0.0332	113	113	0.996	0.00000644	1110
Loss of Function	4.12	10	37.0	0.270	0.00000200	469

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000121	0.000120
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000545	0.0000544
Finnish	0.000142	0.000139
European (Non-Finnish)	0.0000835	0.0000791
Middle Eastern	0.0000545	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

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

• 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_gene_trap: N

Mouse Genome Informatics

• Gene name: Shtn1

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