SDCBP2

syndecan binding protein 2, the group of PDZ domain containing

Basic information

Region (hg38): 20:1309909-1329139

Links

ENSG00000125775 ∙ NCBI:27111 ∙ OMIM:617358 ∙ HGNC:15756 ∙ Uniprot:Q9H190 ∙ 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 SDCBP2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SDCBP2 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			24	1		25
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	24	1	0

Variants in SDCBP2

This is a list of pathogenic ClinVar variants found in the SDCBP2 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-1310458-A-G		not specified	Uncertain significance (Sep 16, 2021)
20-1310476-G-A		not specified	Uncertain significance (Jul 19, 2023)
20-1310812-T-G		not specified	Uncertain significance (Jan 07, 2022)
20-1310852-C-T		not specified	Uncertain significance (May 23, 2023)
20-1310878-A-G		not specified	Likely benign (Aug 14, 2024)
20-1312360-C-G		not specified	Uncertain significance (Jun 22, 2021)
20-1312395-C-A		not specified	Uncertain significance (Feb 14, 2025)
20-1312422-A-C		not specified	Uncertain significance (Apr 04, 2023)
20-1312486-T-C		not specified	Uncertain significance (Oct 02, 2023)
20-1312498-G-A		not specified	Uncertain significance (Feb 12, 2025)
20-1312506-G-A		not specified	Uncertain significance (Apr 19, 2023)
20-1312593-C-T		not specified	Uncertain significance (Nov 25, 2024)
20-1312653-G-A		not specified	Uncertain significance (Sep 07, 2022)
20-1312654-A-C		not specified	Uncertain significance (Aug 08, 2023)
20-1312671-T-A		not specified	Uncertain significance (Feb 14, 2025)
20-1312674-C-T		not specified	Uncertain significance (Oct 22, 2024)
20-1312695-T-C		not specified	Uncertain significance (Dec 27, 2023)
20-1312732-T-G		not specified	Uncertain significance (Jan 03, 2024)
20-1312733-G-C		not specified	Uncertain significance (Dec 14, 2024)
20-1312756-A-G		not specified	Uncertain significance (Jun 07, 2024)
20-1313450-C-G		not specified	Uncertain significance (Dec 13, 2023)
20-1313486-C-T		not specified	Uncertain significance (Aug 27, 2024)
20-1318382-A-G		not specified	Uncertain significance (Jun 27, 2023)
20-1318400-G-A		not specified	Uncertain significance (Sep 11, 2024)
20-1319595-G-A		not specified	Uncertain significance (Sep 14, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SDCBP2	protein_coding	protein_coding	ENST00000360779	8	19265

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.64e-7	0.358	124849	5	894	125748	0.00358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0881	169	172	0.981	0.00000940	1869
Missense in Polyphen		57	56.306	1.0123		643
Synonymous	0.181	74	76.0	0.974	0.00000458	606
Loss of Function	0.550	11	13.2	0.836	5.58e-7	159

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00413	0.00404
Ashkenazi Jewish	0.000209	0.000198
East Asian	0.000109	0.000109
Finnish	0.000623	0.000508
European (Non-Finnish)	0.00500	0.00454
Middle Eastern	0.000109	0.000109
South Asian	0.00797	0.00734
Other	0.00371	0.00343

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Binds phosphatidylinositol 4,5-bisphosphate (PIP2). May play a role in the organization of nuclear PIP2, cell division and cell survival (PubMed:15961997). {ECO:0000269|PubMed:15961997}.

Recessive Scores

• pRec: 0.180

Intolerance Scores

• loftool: 0.732
• rvis_EVS: 1.33
• rvis_percentile_EVS: 94.17

Haploinsufficiency Scores

• pHI: 0.118
• hipred: N
• hipred_score: 0.469
• ghis: 0.404

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.852

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sdcbp2

Zebrafish Information Network

• Gene name: sdcbp2
• Affected structure: post-vent region
• Phenotype tag: abnormal
• Phenotype quality: decreased length

Gene ontology

• Biological process: nervous system development;cell population proliferation;intracellular signal transduction;intracellular transport
• Cellular component: nucleolus;cytoplasm;plasma membrane;nuclear speck;extracellular exosome
• Molecular function: protein binding;phosphatidylinositol-4,5-bisphosphate binding;protein C-terminus binding;identical protein binding;protein homodimerization activity;protein heterodimerization activity