SSH1

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

Basic information

Region (hg38): 12:108778191-108857590

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.

not_specified (148 variants)
not_provided (10 variants)
SSH1-related_disorder (3 variants)
Premature_ovarian_insufficiency (1 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. These statistics are base on transcript: NM_000018984.4. 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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar	1 clinvar	2 clinvar	4
missense			142 clinvar	15 clinvar	2 clinvar	159
nonsense						0
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	147	16	4

Loading clinvar variants...

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
Phenotype

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