SSX2IP

SSX family member 2 interacting protein

Basic information

Region (hg38): 1:84643706-84690803

Links

ENSG00000117155 ∙ NCBI:117178 ∙ OMIM:608690 ∙ HGNC:16509 ∙ Uniprot:Q9Y2D8 ∙ 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 SSX2IP gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SSX2IP 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			32	1		33
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	32	1	0

Variants in SSX2IP

This is a list of pathogenic ClinVar variants found in the SSX2IP region.

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

Position	Type	Phenotype	Significance	ClinVar
1-84647438-G-A		not specified	Uncertain significance (Jan 24, 2024)
1-84647458-T-G		not specified	Uncertain significance (Nov 03, 2023)
1-84647509-C-G		not specified	Uncertain significance (Nov 21, 2022)
1-84647599-T-C		not specified	Likely benign (Nov 15, 2021)
1-84650383-C-T		not specified	Uncertain significance (Jun 05, 2023)
1-84650384-G-A		not specified	Uncertain significance (May 24, 2024)
1-84650426-A-C		not specified	Uncertain significance (Oct 17, 2023)
1-84650438-T-C		not specified	Uncertain significance (Aug 19, 2021)
1-84650461-T-C		not specified	Uncertain significance (Mar 07, 2023)
1-84650471-T-C		not specified	Likely benign (Apr 23, 2024)
1-84650485-T-C		not specified	Uncertain significance (Jan 08, 2024)
1-84650488-G-A		not specified	Uncertain significance (Aug 23, 2021)
1-84650503-A-G		not specified	Uncertain significance (Jul 20, 2022)
1-84651937-T-C		not specified	Uncertain significance (Aug 05, 2024)
1-84655845-C-A		not specified	Uncertain significance (Jul 30, 2024)
1-84655869-C-A		not specified	Uncertain significance (Oct 04, 2024)
1-84655869-C-T		not specified	Uncertain significance (Sep 16, 2021)
1-84655930-G-A		not specified	Uncertain significance (Aug 19, 2024)
1-84655962-A-G		not specified	Uncertain significance (Aug 26, 2024)
1-84656404-C-T		not specified	Uncertain significance (Sep 12, 2023)
1-84656445-A-G		not specified	Uncertain significance (Jun 10, 2024)
1-84656457-T-C		not specified	Uncertain significance (Nov 10, 2022)
1-84656472-T-G		not specified	Uncertain significance (Jul 26, 2022)
1-84656478-T-C		not specified	Uncertain significance (Jul 30, 2024)
1-84662220-C-T		not specified	Uncertain significance (Jul 14, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SSX2IP	protein_coding	protein_coding	ENST00000342203	13	47097

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.31e-9	0.994	125690	0	55	125745	0.000219

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.372	292	310	0.941	0.0000154	4073
Missense in Polyphen		68	89.198	0.76235		1182
Synonymous	0.606	99	107	0.925	0.00000529	1050
Loss of Function	2.54	20	36.6	0.547	0.00000191	440

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000484	0.000482
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.000381	0.000381
Finnish	0.0000924	0.0000924
European (Non-Finnish)	0.000223	0.000220
Middle Eastern	0.000381	0.000381
South Asian	0.000197	0.000196
Other	0.000363	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Belongs to an adhesion system, which plays a role in the organization of homotypic, interneuronal and heterotypic cell-cell adherens junctions (AJs). May connect the nectin-afadin and E- cadherin-catenin system through alpha-actinin and may be involved in organization of the actin cytoskeleton at AJs through afadin and alpha-actinin (By similarity). Involved in cell movement: localizes at the leading edge of moving cells in response to PDGF and is required for the formation of the leading edge and the promotion of cell movement, possibly via activation of Rac signaling (By similarity). Acts as a centrosome maturation factor, probably by maintaining the integrity of the pericentriolar material and proper microtubule nucleation at mitotic spindle poles. The function seems to implicate at least in part WRAP73; the SSX2IP:WRAP73 complex is proposed to act as regulator of spindle anchoring at the mitotic centrosome (PubMed:23816619, PubMed:26545777). Involved in ciliogenesis (PubMed:24356449). It is required for targeted recruitment of the BBSome, CEP290, RAB8, and SSTR3 to the cilia (PubMed:24356449). {ECO:0000250|UniProtKB:Q8VC66, ECO:0000269|PubMed:23816619, ECO:0000269|PubMed:24356449, ECO:0000305|PubMed:26545777}.
• Pathway: Adherens junction - Homo sapiens (human) (Consensus)

Recessive Scores

• pRec: 0.127

Intolerance Scores

• loftool: 0.980
• rvis_EVS: -0.69
• rvis_percentile_EVS: 15.12

Haploinsufficiency Scores

• pHI: 0.167
• hipred: Y
• hipred_score: 0.578
• ghis: 0.617

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.702

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ssx2ip

Zebrafish Information Network

• Gene name: ssx2ipa
• Affected structure: Kupffer's vesicle
• Phenotype tag: abnormal
• Phenotype quality: decreased amount

Gene ontology

• Biological process: centrosome cycle;cell adhesion;regulation of Rac protein signal transduction;intraciliary transport involved in cilium assembly;cilium assembly;regulation of cell motility
• Cellular component: nucleus;cell-cell adherens junction;cell leading edge;protein-containing complex;centriolar satellite;ciliary basal body
• Molecular function: protein binding;protein domain specific binding