SSH2

slingshot protein phosphatase 2, the group of Slingshot protein phosphatases

Basic information

Region (hg38): 17:29625938-29930276

Links

ENSG00000141298 ∙ NCBI:85464 ∙ OMIM:606779 ∙ HGNC:30580 ∙ Uniprot:Q76I76 ∙ 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 SSH2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SSH2 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					2	2
missense			62	2	2	66
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	62	2	4

Variants in SSH2

This is a list of pathogenic ClinVar variants found in the SSH2 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-29630850-A-G			Benign (Mar 29, 2018)
17-29630876-T-C		not specified	Uncertain significance (Jul 14, 2023)
17-29630936-G-T		not specified	Uncertain significance (Aug 11, 2024)
17-29630977-C-T		not specified	Uncertain significance (Aug 01, 2024)
17-29630993-C-T		not specified	Likely benign (Apr 19, 2023)
17-29631038-G-C		not specified	Uncertain significance (Mar 28, 2024)
17-29631061-C-T		not specified	Uncertain significance (May 03, 2023)
17-29631065-A-G		not specified	Uncertain significance (Oct 20, 2024)
17-29631179-C-T			Benign (Mar 29, 2018)
17-29631201-G-T		not specified	Uncertain significance (Sep 30, 2024)
17-29631203-C-T		not specified	Uncertain significance (Dec 03, 2024)
17-29631212-C-T		not specified	Uncertain significance (Dec 26, 2023)
17-29631252-T-A		not specified	Uncertain significance (Jun 29, 2022)
17-29631319-T-C		not specified	Uncertain significance (Sep 01, 2021)
17-29631332-C-T		not specified	Uncertain significance (Dec 03, 2021)
17-29631346-C-T		not specified	Uncertain significance (Aug 16, 2022)
17-29631347-G-A		not specified	Uncertain significance (Apr 05, 2023)
17-29631398-C-T		not specified	Uncertain significance (Jul 20, 2022)
17-29631410-C-A		not specified	Uncertain significance (Jul 12, 2023)
17-29631428-C-T		not specified	Likely benign (Nov 21, 2022)
17-29631488-C-T		not specified	Uncertain significance (Aug 15, 2023)
17-29631544-C-T		not specified	Uncertain significance (Feb 28, 2024)
17-29631613-G-C		not specified	Uncertain significance (Oct 10, 2023)
17-29631673-C-T		not specified	Uncertain significance (Apr 12, 2022)
17-29631695-G-C		not specified	Uncertain significance (Aug 05, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SSH2	protein_coding	protein_coding	ENST00000269033	15	304339

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.997	0.00316	125726	0	22	125748	0.0000875

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.95	612	764	0.801	0.0000397	9366
Missense in Polyphen		135	286.86	0.47062		3397
Synonymous	0.935	269	289	0.930	0.0000149	2779
Loss of Function	6.05	10	61.0	0.164	0.00000352	716

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000268	0.000268
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.0000544	0.0000544
Finnish	0.0000924	0.0000924
European (Non-Finnish)	0.0000528	0.0000527
Middle Eastern	0.0000544	0.0000544
South Asian	0.000163	0.000163
Other	0.00	0.00

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}.
• Pathway: Regulation of actin cytoskeleton - Homo sapiens (human);Axon guidance - Homo sapiens (human);Regulation of Actin Cytoskeleton (Consensus)

Recessive Scores

• pRec: 0.0959

Intolerance Scores

• loftool: 0.379
• rvis_EVS: -0.1
• rvis_percentile_EVS: 45.68

Haploinsufficiency Scores

• pHI: 0.532
• hipred: Y
• hipred_score: 0.558
• ghis: 0.493

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: H
• gene_indispensability_pred: E
• gene_indispensability_score: 0.748

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ssh2

Gene ontology

• Biological process: protein dephosphorylation;regulation of actin polymerization or depolymerization;regulation of lamellipodium assembly;actin cytoskeleton organization;peptidyl-tyrosine dephosphorylation;regulation of axonogenesis
• Cellular component: extracellular space;cytoplasm;cytoskeleton
• Molecular function: actin binding;phosphoprotein phosphatase activity;protein tyrosine phosphatase activity;protein tyrosine/serine/threonine phosphatase activity