SDK1 sidekick cell adhesion molecule 1 [Homo sapiens (human)] - Gene

Summary

Official Symbol: SDK1provided by HGNC
Official Full Name: sidekick cell adhesion molecule 1provided by HGNC
Primary source: HGNC:HGNC:19307
See related: Ensembl:ENSG00000146555 MIM:607216; AllianceGenome:HGNC:19307
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Summary: The protein encoded by this gene is a member of the immunoglobulin superfamily. The protein contains six immunoglobulin-like domains and thirteen fibronectin type III domains. Fibronectin type III domains are present in both extracellular and intracellular proteins and tandem repeats are known to contain binding sites for DNA, heparin and the cell surface. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2016]
Expression: Broad expression in endometrium (RPKM 2.3), spleen (RPKM 2.1) and 22 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 7p22.2

Exon count:: 46

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	7	NC_000007.14 (3301252..4269000)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	7	NC_060931.1 (3415529..4385763)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	7	NC_000007.13 (3340884..4308632)

Chromosome 7 - NC_000007.14 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Novel loci for ocular axial length identified through extreme-phenotype genome-wide association study in Chinese populations.
Title: Novel loci for ocular axial length identified through extreme-phenotype genome-wide association study in Chinese populations.
SDK1 could possibly serve as a candidate gene for alterations associated with asbestos exposure.
Title: Driver Gene and Novel Mutations in Asbestos-Exposed Lung Adenocarcinoma and Malignant Mesothelioma Detected by Exome Sequencing.
Case-control studies reveal malignant mesothelioma risk associated with variants in the SDK1, CRTAM and RASGRF2 genes.
Title: A genome-wide association study for malignant mesothelioma risk.
Data conclude that the up-regulation of sdk-1 in podocytes is an important pathogenic factor in glomerulosclerosis and that the mechanism involves disruption of the actin cytoskeleton possibly via alterations in MAGI-1 function.
Title: Up-regulation of the homophilic adhesion molecule sidekick-1 in podocytes contributes to glomerulosclerosis.
Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
SDK1 may be a susceptibility gene for hypertension in Japanese individuals, although the functional relevance of the identified polymorphism was not determined.
Title: Assessment of a polymorphism of SDK1 with hypertension in Japanese Individuals.
Observational study of gene-disease association. (HuGE Navigator)
Title: Comprehensive copy number variant (CNV) analysis of neuronal pathways genes in psychiatric disorders identifies rare variants within patients.
dysregulation of sdk-1 protein may play an important role in HIV-associated nephropathy pathogenesis
Title: Sidekick-1 is upregulated in glomeruli in HIV-associated nephropathy.

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Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
Genome-wide association studies in an isolated founder population from the Pacific Island of Kosrae. EBI GWAS Catalog EBI GWAS CatalogPubMed
Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

GDB:4585491 (e-PCR)
- UniSTS:56064

RH119531 (e-PCR)
- UniSTS:132614

RH11955 (e-PCR)
- UniSTS:73739

D7S2391 (e-PCR)
- UniSTS:154126

GDB:1318258 (e-PCR)
- UniSTS:40463

GDB:1318462 (e-PCR)
- UniSTS:47119

SHGC-83254 (e-PCR)
- UniSTS:101140

WI-18580 (e-PCR)
- UniSTS:43041

D7S2134E (e-PCR)
- UniSTS:33318

GDB:1318732 (e-PCR)
- UniSTS:74039

GDB:1318166 (e-PCR)
- UniSTS:79419

RH93095 (e-PCR)
- UniSTS:90428

D7S752 (e-PCR)
- UniSTS:5699

D7S2424 (e-PCR), detects polymorphism
- UniSTS:39239

D7S544E (e-PCR)
- UniSTS:75084

A009E45 (e-PCR)
- UniSTS:3409

G32491 (e-PCR)
- UniSTS:117076

GDB:1317614 (e-PCR)
- UniSTS:53589

GDB:1318720 (e-PCR)
- UniSTS:40534

RH104326 (e-PCR)
- UniSTS:98651

D7S2424 (e-PCR), detects polymorphism
- UniSTS:17756

D7S544E (e-PCR)
- UniSTS:19807

GDB:1318168 (e-PCR)
- UniSTS:56683

SGC35203 (e-PCR)
- UniSTS:42626

WI-10377 (e-PCR)
- UniSTS:17027

D7S2236 (e-PCR)
- UniSTS:72582

SHGC-33107 (e-PCR)
- UniSTS:65158

D7S2649 (e-PCR)
- UniSTS:76696

STS-N26031 (e-PCR)
- UniSTS:71075

STS-N20093 (e-PCR)
- UniSTS:3755

GDB:1317626 (e-PCR)
- UniSTS:16300

G20798 (e-PCR)
- UniSTS:68799

A006H07 (e-PCR)
- UniSTS:68800

RH16383 (e-PCR)
- UniSTS:42688

WI-12220 (e-PCR)
- UniSTS:83137

SHGC-111082 (e-PCR)
- UniSTS:168129

RH11998 (e-PCR)
- UniSTS:10690

GDB:1318252 (e-PCR)
- UniSTS:17628

SHGC-154026 (e-PCR)
- UniSTS:184549

SHGC-154245 (e-PCR)
- UniSTS:184552

RH102158 (e-PCR)
- UniSTS:96492

GDB:1317130 (e-PCR)
- UniSTS:44786

A004G34 (e-PCR)
- UniSTS:66807

GDB:1317596 (e-PCR)
- UniSTS:58616

SHGC-145460 (e-PCR)
- UniSTS:174588

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables identical protein binding	ISS Inferred from Sequence or Structural Similarity more info

Process	Evidence Code	Pubs
involved_in behavioral response to cocaine	IEA Inferred from Electronic Annotation more info
involved_in homophilic cell adhesion via plasma membrane adhesion molecules	IBA Inferred from Biological aspect of Ancestor more info
involved_in homophilic cell adhesion via plasma membrane adhesion molecules	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of dendritic spine development	IEA Inferred from Electronic Annotation more info
involved_in retina layer formation	ISS Inferred from Sequence or Structural Similarity more info
involved_in synapse assembly	IBA Inferred from Biological aspect of Ancestor more info
involved_in synapse assembly	ISS Inferred from Sequence or Structural Similarity more info

Component	Evidence Code	Pubs
located_in plasma membrane	TAS Traceable Author Statement more info
is_active_in synapse	IBA Inferred from Biological aspect of Ancestor more info
located_in synapse	ISS Inferred from Sequence or Structural Similarity more info

General protein information

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Preferred Names: protein sidekick-1

Names: sidekick homolog 1, cell adhesion molecule

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

NG_051298.1 RefSeqGene

Range

4805..972553

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001079653.2 → NP_001073121.1 protein sidekick-1 isoform 2

Status: REVIEWED

Description

Transcript Variant: This variant (2) differs in the 5' UTR, lacks several exons in the 5' coding region, uses a downstream in-frame start codon, and differs in the 3' coding region and 3' UTR, compared to variant 1. The encoded isoform (2) has a significantly shorter N-terminus and a distinct C-terminus, compared to isoform 1.

Source sequence(s)

AL833354, DB065853, DB454012

Related

ENST00000476701.5

Conserved Domains (1) summary

cd00063
Location:191 → 284

FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...
NM_152744.4 → NP_689957.3 protein sidekick-1 isoform 1

See identical proteins and their annotated locations for NP_689957.3

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).

Source sequence(s)

AC015968, AC017000, AC073316, AL833354, AY310398, DB065853

Consensus CDS

CCDS34590.1

UniProtKB/Swiss-Prot

Q7Z5N4, Q8TEN9, Q8TEP5, Q96N44

UniProtKB/TrEMBL

F8W6X9

Related

ENSP00000385899.2, ENST00000404826.7

Conserved Domains (6) summary

cd00096
Location:404 → 472

Ig; Immunoglobulin domain

smart00408
Location:312 → 364

IGc2; Immunoglobulin C-2 Type

cd00063
Location:1704 → 1797

FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...

pfam07679
Location:480 → 570

I-set; Immunoglobulin I-set domain

pfam00041
Location:771 → 857

fn3; Fibronectin type III domain

cl11960
Location:494 → 570

Ig; Immunoglobulin domain

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000007.14 Reference GRCh38.p14 Primary Assembly

Range

3301252..4269000

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_047420038.1 → XP_047275994.1 protein sidekick-1 isoform X4
XM_047420037.1 → XP_047275993.1 protein sidekick-1 isoform X3
XM_024446683.2 → XP_024302451.1 protein sidekick-1 isoform X1

UniProtKB/TrEMBL

F8W6X9

Conserved Domains (6) summary

cd00063
Location:1453 → 1546

FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...

pfam07679
Location:229 → 319

I-set; Immunoglobulin I-set domain

pfam00041
Location:722 → 803

fn3; Fibronectin type III domain

pfam13927
Location:42 → 113

Ig_3; Immunoglobulin domain

cl11960
Location:329 → 413

Ig; Immunoglobulin domain

cl28434
Location:135 → 224

I-set; Immunoglobulin I-set domain
XM_024446684.2 → XP_024302452.1 protein sidekick-1 isoform X2

UniProtKB/TrEMBL

F8W6X9

Conserved Domains (6) summary

cd00063
Location:1433 → 1526

FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...

pfam07679
Location:229 → 319

I-set; Immunoglobulin I-set domain

pfam00041
Location:722 → 803

fn3; Fibronectin type III domain

pfam13927
Location:42 → 113

Ig_3; Immunoglobulin domain

cl11960
Location:329 → 413

Ig; Immunoglobulin domain

cl28434
Location:135 → 224

I-set; Immunoglobulin I-set domain