SSH1

slingshot protein phosphatase 1, the group of Slingshot protein phosphatases|MicroRNA protein coding host genes

Basic information

Region (hg38): 12:108778190-108857590

Links

ENSG00000084112 ∙ NCBI:54434 ∙ OMIM:606778 ∙ HGNC:30579 ∙ Uniprot:Q8WYL5 ∙ 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 SSH1 gene.

• Inborn genetic diseases (43 variants)
• not provided (8 variants)
• not specified (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SSH1 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	2
missense			40	7	2	49
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1	1	2
non coding						0
Total	0	0	40	8	3

Variants in SSH1

This is a list of pathogenic ClinVar variants found in the SSH1 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-108788024-T-G		not specified	Uncertain significance (Feb 23, 2023)
12-108788115-G-A		not specified	Uncertain significance (Mar 01, 2023)
12-108788156-A-C			Likely benign (May 15, 2018)
12-108788305-G-A		not specified	Uncertain significance (Jun 11, 2021)
12-108788368-T-A		not specified	Uncertain significance (Sep 23, 2023)
12-108788371-G-A		not specified	Uncertain significance (Aug 11, 2022)
12-108788382-A-G		not specified	Uncertain significance (Jul 11, 2022)
12-108788422-C-T		not specified	Uncertain significance (Mar 31, 2023)
12-108788427-C-T		not specified	Uncertain significance (Jul 14, 2022)
12-108788481-G-T		not specified	Uncertain significance (Jan 27, 2022)
12-108788482-C-T		not specified	Uncertain significance (Nov 19, 2022)
12-108788506-C-T		not specified	Uncertain significance (Mar 29, 2023)
12-108788541-T-G		not specified	Uncertain significance (May 31, 2023)
12-108788580-G-A		not specified	Uncertain significance (Aug 02, 2022)
12-108788619-G-C		not specified	Uncertain significance (Oct 27, 2023)
12-108788869-A-C		not specified	Uncertain significance (Dec 18, 2023)
12-108788877-G-A		SSH1-related disorder	Likely benign (Feb 10, 2022)
12-108788896-G-A		not specified	Uncertain significance (Dec 11, 2023)
12-108788995-G-C			Benign (Dec 31, 2019)
12-108789000-G-A		not specified	Likely benign (Aug 12, 2021)
12-108789021-G-C		not specified	Uncertain significance (Sep 20, 2023)
12-108789029-C-G		not specified	Uncertain significance (May 10, 2022)
12-108789036-G-A		not specified	Likely benign (Feb 28, 2024)
12-108789042-C-T		not specified	Uncertain significance (Nov 06, 2023)
12-108789048-C-T		not specified	Uncertain significance (Sep 16, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SSH1	protein_coding	protein_coding	ENST00000326495	15	74901

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000330	1.00	125699	0	49	125748	0.000195

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.02	540	611	0.884	0.0000379	6891
Missense in Polyphen		96	168.67	0.56916		1880
Synonymous	-0.549	266	255	1.04	0.0000174	2072
Loss of Function	3.99	14	41.8	0.335	0.00000233	485

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000876	0.000830
Ashkenazi Jewish	0.00	0.00
East Asian	0.000172	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.000176	0.000176
Middle Eastern	0.000172	0.000163
South Asian	0.000163	0.000163
Other	0.000717	0.000652

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Protein phosphatase which regulates actin filament dynamics. Dephosphorylates and activates the actin binding/depolymerizing factor cofilin, which subsequently binds to actin filaments and stimulates their disassembly. Inhibitory phosphorylation of cofilin is mediated by LIMK1, which may also be dephosphorylated and inactivated by this protein. {ECO:0000269|PubMed:11832213, ECO:0000269|PubMed:12684437, ECO:0000269|PubMed:12807904, ECO:0000269|PubMed:14531860, ECO:0000269|PubMed:14645219, ECO:0000269|PubMed:15056216, ECO:0000269|PubMed:15159416, ECO:0000269|PubMed:15660133, ECO:0000269|PubMed:15671020, ECO:0000269|PubMed:16230460}.
• Pathway: Regulation of actin cytoskeleton - Homo sapiens (human);Axon guidance - Homo sapiens (human);Regulation of Actin Cytoskeleton;CXCR4-mediated signaling events;FGF signaling pathway (Consensus)

Recessive Scores

• pRec: 0.115

Intolerance Scores

• loftool: 0.556
• rvis_EVS: -0.37
• rvis_percentile_EVS: 28.31

Haploinsufficiency Scores

• pHI: 0.111
• hipred: Y
• hipred_score: 0.792
• ghis: 0.503

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.916

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ssh1

Gene ontology

• Biological process: cell morphogenesis;protein dephosphorylation;regulation of actin polymerization or depolymerization;regulation of lamellipodium assembly;actin cytoskeleton organization;positive regulation of synaptic plasticity;regulation of cellular protein metabolic process;peptidyl-tyrosine dephosphorylation;regulation of axonogenesis;cellular response to ATP;excitatory chemical synaptic transmission;positive regulation of neuron death;positive regulation of AMPA glutamate receptor clustering;positive regulation of vascular associated smooth muscle cell migration;positive regulation of excitatory postsynaptic potential
• Cellular component: cytoplasm;cytosol;cytoskeleton;plasma membrane;lamellipodium;growth cone;midbody;cleavage furrow
• Molecular function: actin binding;phosphoprotein phosphatase activity;protein tyrosine phosphatase activity;protein binding;protein tyrosine/serine/threonine phosphatase activity