SDCBP2

protein-coding

syndecan binding protein 2, the group of PDZ domain containing

Gene summary

The protein encoded by this gene contains two class II PDZ domains. PDZ domains facilitate protein-protein interactions by binding to the cytoplasmic C-terminus of transmembrane proteins, and PDZ-containing proteins mediate cell signaling and the organization of protein complexes. The encoded protein binds to phosphatidylinositol 4, 5-bisphosphate (PIP2) and plays a role in nuclear PIP2 organization and cell division. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. Read-through transcription also exists between this gene and the upstream FKBP1A (FK506 binding protein 1A, 12kDa) gene, as represented in GeneID:100528031. [provided by RefSeq, Sep 2011]

MANE transcript

NM_080489.5

Inheritance

—

ClinVar variants

U:43B:1

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.84

Max pathogenic AF

—

Genomic locus

chr20:1,309,909-1,329,139

External References & Databases

Ensembl (ENSG00000125775)

Transcript & Mutation Effects

hg38 • Region Span ~19.2 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to SDCBP2 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 44

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_080489.5. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			43 clinvar	1 clinvar		44
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	43	1	0	44

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 32 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_080489.5	RefSeq	NP_536737.3	8	MANE Select
ENST00000360779.4	Ensembl	ENSP00000354013.3	8	MANE Select
NM_001199784.2	RefSeq	NP_001186713.1	8	Standard
NM_015685.6	RefSeq	NP_056500.2	5	Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / Model	Organism	Observed Phenotype
sdcbp2	Danio rerio	Structure: post-vent region Quality: decreased length abnormal

Gene / Model

Organism

Observed Phenotype

sdcbp2

Danio rerio

Structure: post-vent region

Quality: decreased length

abnormal

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

nervous system development
cell population proliferation
intracellular signal transduction
intracellular transport

Molecular Function

protein binding
phosphatidylinositol-4,5-bisphosphate binding
protein C-terminus binding
identical protein binding
protein homodimerization activity

Cellular Component

nucleolus
cytoplasm
plasma membrane
nuclear speck
extracellular exosome

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000360779
Coding exons: 8
Length: 19265
Individuals with no LoFs: 124849
Homozygous LoFs: 5
Heterozygous LoFs: 894
Defined: 125748
p: 0.00358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.0881	169	172	0.981	0.00000940	1869
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00071	0.00062	rare
Latino/Admixed American	0.0034	0.0033	notable
Ashkenazi Jewish	0.00021	0.00020	rare
East Asian	0.00011	0.00011	rare
Finnish	0.00062	0.00051	rare
European (Non-Finnish)	0.0050	0.0045	notable
South Asian	0.0080	0.0073	notable
Other	0.0037	0.0034	notable

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.852

Gene Damage Prediction

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