SSH3

slingshot protein phosphatase 3, the group of Slingshot protein phosphatases

Basic information

Region (hg38): 11:67303478-67312607

Links

ENSG00000172830 ∙ NCBI:54961 ∙ OMIM:606780 ∙ HGNC:30581 ∙ Uniprot:Q8TE77 ∙ 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 SSH3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SSH3 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						0
missense			66	4		70
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	66	4	0

Variants in SSH3

This is a list of pathogenic ClinVar variants found in the SSH3 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-67303632-C-A		not specified	Uncertain significance (Jan 06, 2023)
11-67303656-C-T		not specified	Uncertain significance (Nov 15, 2021)
11-67303657-C-T		not specified	Uncertain significance (Apr 25, 2022)
11-67303683-G-A		not specified	Uncertain significance (Apr 18, 2023)
11-67304793-G-T		not specified	Uncertain significance (Aug 19, 2024)
11-67304837-G-A		not specified	Uncertain significance (Jul 28, 2021)
11-67304862-C-T		not specified	Uncertain significance (Jul 31, 2024)
11-67304874-C-T		not specified	Uncertain significance (Aug 09, 2021)
11-67304960-C-G		not specified	Uncertain significance (Jul 31, 2024)
11-67304963-C-T		not specified	Uncertain significance (Nov 25, 2024)
11-67305002-C-T		not specified	Uncertain significance (Jul 06, 2021)
11-67306871-C-A		not specified	Uncertain significance (Sep 25, 2023)
11-67306893-C-T		not specified	Uncertain significance (Jul 19, 2023)
11-67306896-C-A		not specified	Uncertain significance (Oct 13, 2023)
11-67306901-G-A		not specified	Uncertain significance (Nov 12, 2024)
11-67306924-T-A		not specified	Likely benign (Nov 07, 2022)
11-67306925-G-A		not specified	Uncertain significance (May 17, 2023)
11-67306926-A-T		not specified	Uncertain significance (May 17, 2023)
11-67306940-G-T		not specified	Uncertain significance (Sep 26, 2022)
11-67307044-C-A		not specified	Uncertain significance (Mar 05, 2024)
11-67307047-C-T		not specified	Uncertain significance (Jan 16, 2024)
11-67307061-G-C		not specified	Uncertain significance (Dec 14, 2024)
11-67307072-G-C		not specified	Uncertain significance (Sep 14, 2022)
11-67307372-G-A		not specified	Uncertain significance (Dec 31, 2023)
11-67307414-C-G		not specified	Uncertain significance (Aug 02, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SSH3	protein_coding	protein_coding	ENST00000308127	14	9160

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.47e-14	0.457	125610	0	138	125748	0.000549

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.600	371	405	0.916	0.0000251	4238
Missense in Polyphen		135	151.72	0.88978		1578
Synonymous	0.461	156	163	0.954	0.00000994	1349
Loss of Function	1.47	26	35.4	0.734	0.00000180	349

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00124	0.00123
Ashkenazi Jewish	0.000300	0.000298
East Asian	0.000871	0.000870
Finnish	0.000328	0.000323
European (Non-Finnish)	0.000487	0.000484
Middle Eastern	0.000871	0.000870
South Asian	0.000622	0.000621
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Protein phosphatase which may play a role in the regulation of actin filament dynamics. Can dephosphorylate and activate the actin binding/depolymerizing factor cofilin, which subsequently binds to actin filaments and stimulates their disassembly (By similarity). {ECO:0000250}.
• Pathway: Regulation of actin cytoskeleton - Homo sapiens (human);Axon guidance - Homo sapiens (human);Regulation of Actin Cytoskeleton (Consensus)

Recessive Scores

• pRec: 0.0973

Intolerance Scores

• loftool: 0.592
• rvis_EVS: -0.77
• rvis_percentile_EVS: 13.15

Haploinsufficiency Scores

• pHI: 0.509
• hipred: N
• hipred_score: 0.489
• ghis: 0.526

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.507

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ssh3
• Phenotype: normal phenotype

Gene ontology

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