SIL1 SIL1 nucleotide exchange factor [Homo sapiens (human)] - Gene

Summary

Official Symbol: SIL1provided by HGNC
Official Full Name: SIL1 nucleotide exchange factorprovided by HGNC
Primary source: HGNC:HGNC:24624
See related: Ensembl:ENSG00000120725 MIM:608005; AllianceGenome:HGNC:24624
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
Also known as: BAP; MSS; ULG5
Summary: This gene encodes a resident endoplasmic reticulum (ER), N-linked glycoprotein with an N-terminal ER targeting sequence, 2 putative N-glycosylation sites, and a C-terminal ER retention signal. This protein functions as a nucleotide exchange factor for another unfolded protein response protein. Mutations in this gene have been associated with Marinesco-Sjogren syndrome. Alternate transcriptional splice variants have been characterized. [provided by RefSeq, Jul 2008]
Expression: Ubiquitous expression in testis (RPKM 23.5), thyroid (RPKM 19.7) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 5q31.2

Exon count:: 13

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	5	NC_000005.10 (138946724..139198368, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	5	NC_060929.1 (139472860..139724442, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	5	NC_000005.9 (138282413..138534057, complement)

Chromosome 5 - NC_000005.10 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 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?

Exome sequencing revealed variants in SGCA and SIL1 genes underlying limb girdle muscular dystrophy and Marinesco-Sjogren syndrome patients.
Title: Exome sequencing revealed variants in SGCA and SIL1 genes underlying limb girdle muscular dystrophy and Marinesco-Sjögren syndrome patients.
Down-Regulation and Clinic-Pathological Correlation of SIK-1 and SIL-1-LNC in Non-Small Cell Lung Cancer Patients.
Title: Down-regulation and Clinic-pathological Correlation of SIK-1 and SIK-1-LNC in Non-small Cell Lung Cancer Patients.
Nucleotide exchange factor SIL1 promotes the progress of breast cancer cells via regulating the cell cycle and apoptosis.
Title: Nucleotide exchange factor SIL1 promotes the progress of breast cancer cells via regulating the cell cycle and apoptosis.
Proteomic Analysis of Marinesco-Sjogren Syndrome Fibroblasts Indicates Pro-Survival Metabolic Adaptation to SIL1 Loss.
Title: Proteomic Analysis of Marinesco-Sjogren Syndrome Fibroblasts Indicates Pro-Survival Metabolic Adaptation to SIL1 Loss.
SIL1 deficiency causes degenerative changes of peripheral nerves and neuromuscular junctions in fish, mice and human. The data expand the spectrum of tissues affected by SIL1-loss and suggest that impaired neuromuscular transmission might be part of Marinesco-Sjogren Syndrome pathophysiology.
Title: SIL1 deficiency causes degenerative changes of peripheral nerves and neuromuscular junctions in fish, mice and human.
single-molecule FRET experiments with mammalian proteins reveal that Bap affects the conformation of both BiP domains, including the lid subdomain, which is important for substrate binding
Title: Bap (Sil1) regulates the molecular chaperone BiP by coupling release of nucleotide and substrate.
Findings indicate that SIL1 deficiency alters secretory transport, potentially contributing to the cellular pathology of Marinesco-Sjogren syndrome.
Title: PERK inhibition attenuates the abnormalities of the secretory pathway and the increased apoptotic rate induced by SIL1 knockdown in HeLa cells.
SIL1-depleted HEK293 cells are an appropriate model to identify proteins modulated by SIL1 expression level.
Title: Cellular Signature of SIL1 Depletion: Disease Pathogenesis due to Alterations in Protein Composition Beyond the ER Machinery.
In a child with Marinesco-Sjogren syndrome it was found that a mutation in SIL1 affected the 5' UTR, translation initiation site and the endoplasmic reticulum-targeting signal sequence.
Title: Marinesco-Sjögren Syndrome in an Emirati Child with a Novel Mutation in SIL1 Affecting the 5' Untranslated Region.
this case study is the first report on Chinese Marinesco-Sjogren syndrome (MSS) patients, MSS complicated by Dandy-Walker syndrome (DWS), and a nonstop mutation in SIL1; our findings imply the pathogenetic association between DWS and MSS
Title: Novel SIL1 nonstop mutation in a Chinese consanguineous family with Marinesco-Sjögren syndrome and Dandy-Walker syndrome.

Submit: New GeneRIF Correction See all GeneRIFs (26)

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

Associated conditions

Description	Tests
Marinesco-Sjogren syndrome MedGen: C0024814 OMIM: 248800 GeneReviews: Marinesco-Sjogren Syndrome	Compare labs

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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Protein interactions

Protein	Gene	Interaction	Pubs
Envelope surface glycoprotein gp160, precursor	env	HIV-1 gp160 interacts with SIL1; predicted interaction to be within the endoplasmic reticulum and function as chaperone for endoplasmic reticulum-associated degradation	PubMed

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Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

bac5235T (e-PCR)
- UniSTS:181569

bac5237T (e-PCR)
- UniSTS:181573

D5S1372 (e-PCR)
- UniSTS:39559

RH91427 (e-PCR)
- UniSTS:85199

STS-W04672 (e-PCR)
- UniSTS:83166

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables adenyl-nucleotide exchange factor activity	IBA Inferred from Biological aspect of Ancestor more info
enables adenyl-nucleotide exchange factor activity	IDA Inferred from Direct Assay more info	PubMed
enables identical protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables unfolded protein binding	NAS Non-traceable Author Statement more info	PubMed

Process	Evidence Code	Pubs
involved_in cotranslational protein targeting to membrane	ISS Inferred from Sequence or Structural Similarity more info
involved_in intracellular protein transport	NAS Non-traceable Author Statement more info	PubMed
involved_in protein folding	NAS Non-traceable Author Statement more info	PubMed

Component	Evidence Code	Pubs
is_active_in endoplasmic reticulum	IBA Inferred from Biological aspect of Ancestor more info
located_in endoplasmic reticulum	IDA Inferred from Direct Assay more info	PubMed
located_in endoplasmic reticulum	NAS Non-traceable Author Statement more info	PubMed
located_in endoplasmic reticulum lumen	IEA Inferred from Electronic Annotation more info
located_in extracellular space	HDA more info	PubMed

General protein information

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Preferred Names: nucleotide exchange factor SIL1

Names: BiP-associated protein; SIL1 homolog, endoplasmic reticulum chaperone; SIL1-like protein endoplasmic reticulum chaperone

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_008112.2 RefSeqGene

Range

5009..256653

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001037633.2 → NP_001032722.1 nucleotide exchange factor SIL1 precursor

See identical proteins and their annotated locations for NP_001032722.1

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longer transcript. Variants 1 and 2 encode the same protein.

Source sequence(s)

AC008614, AC011378, AC011405, CA415266, CB125000, CD369479

Consensus CDS

CCDS4209.1

UniProtKB/Swiss-Prot

D3DQC2, Q8N2L3, Q9H173

UniProtKB/TrEMBL

A0A0S2Z6B4, D6REA1

Related

ENSP00000265195.5, ENST00000265195.9

Conserved Domains (1) summary

pfam08609
Location:192 → 222

Fes1; Nucleotide exchange factor Fes1
NM_022464.5 → NP_071909.1 nucleotide exchange factor SIL1 precursor

See identical proteins and their annotated locations for NP_071909.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) lacks an exon in the 5'UTR compared to variant 1. Variants 1 and 2 encode the same protein.

Source sequence(s)

AK074624, BC011568, CA415266, CD369479

Consensus CDS

CCDS4209.1

UniProtKB/Swiss-Prot

D3DQC2, Q8N2L3, Q9H173

UniProtKB/TrEMBL

A0A0S2Z6B4, D6REA1

Related

ENSP00000378294.2, ENST00000394817.7

Conserved Domains (1) summary

pfam08609
Location:192 → 222

Fes1; Nucleotide exchange factor Fes1

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_000005.10 Reference GRCh38.p14 Primary Assembly

Range

138946724..139198368 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_011543570.3 → XP_011541872.1 nucleotide exchange factor SIL1 isoform X1

UniProtKB/TrEMBL

D6REA1

Conserved Domains (1) summary

pfam08609
Location:203 → 232

Fes1; Nucleotide exchange factor Fes1
XM_047417498.1 → XP_047273454.1 nucleotide exchange factor SIL1 isoform X2

UniProtKB/Swiss-Prot

D3DQC2, Q8N2L3, Q9H173

UniProtKB/TrEMBL

A0A0S2Z6B4
XM_047417496.1 → XP_047273452.1 nucleotide exchange factor SIL1 isoform X1

Alternate T2T-CHM13v2.0

Genomic

NC_060929.1 Alternate T2T-CHM13v2.0

Range

139472860..139724442 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054353098.1 → XP_054209073.1 nucleotide exchange factor SIL1 isoform X1
XM_054353100.1 → XP_054209075.1 nucleotide exchange factor SIL1 isoform X2

UniProtKB/Swiss-Prot

D3DQC2, Q8N2L3, Q9H173

UniProtKB/TrEMBL

A0A0S2Z6B4
XM_054353099.1 → XP_054209074.1 nucleotide exchange factor SIL1 isoform X1