SBF1 SET binding factor 1 [Homo sapiens (human)] - Gene

Summary

Official Symbol: SBF1provided by HGNC
Official Full Name: SET binding factor 1provided by HGNC
Primary source: HGNC:HGNC:10542
See related: Ensembl:ENSG00000100241 MIM:603560; AllianceGenome:HGNC:10542
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: MTMR5; CMT4B3; DENND7A
Summary: This gene encodes a member of the protein-tyrosine phosphatase family. However, the encoded protein does not appear to be a catalytically active phosphatase because it lacks several amino acids in the catalytic pocket. This protein contains a Guanine nucleotide exchange factor (GEF) domain which is necessary for its role in growth and differentiation. Mutations in this gene have been associated with Charcot-Marie-Tooth disease 4B3. Pseudogenes of this gene have been defined on chromosomes 1 and 8. [provided by RefSeq, Dec 2014]
Expression: Broad expression in testis (RPKM 38.3), brain (RPKM 19.4) and 24 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 22q13.33

Exon count:: 41

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	22	NC_000022.11 (50445000..50475035, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	22	NC_060946.1 (50954193..50984219, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	22	NC_000022.10 (50883429..50913464, complement)

Chromosome 22 - NC_000022.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

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?

A (GCC) repeat in SBF1 reveals a novel biological phenomenon in human and links to late onset neurocognitive disorder.
Title: A (GCC) repeat in SBF1 reveals a novel biological phenomenon in human and links to late onset neurocognitive disorder.
A novel frameshift deletion in autosomal recessive SBF1-related syndromic neuropathy with necklace fibres.
Title: A novel frameshift deletion in autosomal recessive SBF1-related syndromic neuropathy with necklace fibres.
The novel SBF1 null mutation highlights distinct severe phenotypic manifestations, broadening the clinical spectrum of SBF1-related neuropathies: cerebellar and pyramidal signs evident in the first months of life with peripheral polyneuropathy emerging only toward the end of the first decade, together with unique MRI findings.
Title: Novel SBF1 splice-site null mutation broadens the clinical spectrum of Charcot-Marie-Tooth type 4B3 disease.
Novel sequence variants in SBF1 (c.1168C>G and c.2209_2210del) as the potential causative mutations in two siblings with severe axonal neuropathy, hearing loss, facial weakness and bulbar features.
Title: SBF1 mutations associated with autosomal recessive axonal neuropathy with cranial nerve involvement.
ZNF195 and SBF1 are potential biomarkers for gemcitabine sensitivity in head and neck squamous cell carcinoma cell lines.
Title: DNA microarray reveals ZNF195 and SBF1 are potential biomarkers for gemcitabine sensitivity in head and neck squamous cell carcinoma cell lines.
Compound heterozygous mutations in SBF1 appear to be the underlying causes of a novel Charcot-Marie-Tooth disease type 4B subtype (designated as CMT4B3) in a Korean family.
Title: SET binding factor 1 (SBF1) mutation causes Charcot-Marie-Tooth disease type 4B3.
SBF1 (MTMR5) belongs to the myotubularin family of phosphoinositides phosphatases-like
Title: Characterization of the myotubularin dual specificity phosphatase gene family from yeast to human.
Observational study of gene-disease association. (HuGE Navigator)
Title: Association of genetic variants with hemorrhagic stroke in Japanese individuals.
MTMR2 interacts with MTMR5 via its coiled-coil domain and that mutations in the coiled-coil domain of either MTMR2 or MTMR5 abrogate this interaction.
Title: Regulation of myotubularin-related (MTMR)2 phosphatidylinositol phosphatase by MTMR5, a catalytically inactive phosphatase.

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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

Associated conditions

Description	Tests
Charcot-Marie-Tooth disease type 4 MedGen: C4082197 GeneReviews: Charcot-Marie-Tooth Hereditary Neuropathy Overview	not available
Charcot-Marie-Tooth disease type 4B3 MedGen: C3695063 OMIM: 615284 GeneReviews: Not available	not available

EBI GWAS Catalog

Description
Loci associated with N-glycosylation of human immunoglobulin G show pleiotropy with autoimmune diseases and haematological cancers. 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

RH46917 (e-PCR)
- UniSTS:53761

STS-T23637 (e-PCR)
- UniSTS:64529

RH47520 (e-PCR)
- UniSTS:89695

RH11296 (e-PCR)
- UniSTS:87943

SBF1_8611 (e-PCR)
- UniSTS:467869

RH47771 (e-PCR)
- UniSTS:44724

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables guanyl-nucleotide exchange factor activity	IBA Inferred from Biological aspect of Ancestor more info
enables guanyl-nucleotide exchange factor activity	IDA Inferred from Direct Assay more info	PubMed
enables guanyl-nucleotide exchange factor activity	TAS Traceable Author Statement more info
NOT enables phosphatase activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables protein tyrosine/serine/threonine phosphatase activity	TAS Traceable Author Statement more info	PubMed

Process	Evidence Code	Pubs
involved_in protein dephosphorylation	TAS Traceable Author Statement more info	PubMed
involved_in spermatid development	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
is_active_in cytoplasm	IBA Inferred from Biological aspect of Ancestor more info
located_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in cytosol	TAS Traceable Author Statement more info
located_in endoplasmic reticulum membrane	TAS Traceable Author Statement more info
is_active_in membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in membrane	TAS Traceable Author Statement more info	PubMed
located_in neuron projection	IEA Inferred from Electronic Annotation more info
located_in nuclear body	IDA Inferred from Direct Assay more info
located_in perinuclear region of cytoplasm	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: myotubularin-related protein 5

Names: DENN/MADD domain containing 7A; inactive phosphatidylinositol 3-phosphatase 5

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_041810.1 RefSeqGene

Range

5037..35072

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001365819.1 → NP_001352748.1 myotubularin-related protein 5 isoform 2

Status: REVIEWED

Source sequence(s)

AL096767

Consensus CDS

CCDS93186.1

UniProtKB/Swiss-Prot

A0A024R4Z9, A6PVG9, G5E933, O60228, O95248, Q5JXD8, Q5PPM2, Q96GR9, Q9UGB8

UniProtKB/TrEMBL

A0A8I5KXX8

Related

ENSP00000510414.1, ENST00000689129.1

Conserved Domains (7) summary

smart00801
Location:365 → 433

dDENN; Domain always found downstream of DENN domain, found in a variety of signalling proteins

smart00799
Location:130 → 311

DENN; Domain found in a variety of signalling proteins, always encircled by uDENN and dDENN

smart00800
Location:1 → 86

uDENN; Domain always found upstream of DENN domain, found in a variety of signalling proteins

cd01235
Location:1761 → 1866

PH_Sbf1_hMTMR5; Set binding factor 1 (also called Human MTMR5) Pleckstrin Homology (PH) domain

pfam06602
Location:1129 → 1532

Myotub-related; Myotubularin-like phosphatase domain

pfam12335
Location:544 → 765

SBF2; Myotubularin protein

cl17171
Location:894 → 1012

PH-like; Pleckstrin homology-like domain
NM_001410794.1 → NP_001397723.1 myotubularin-related protein 5 isoform 3

Status: REVIEWED

Source sequence(s)

AL096767

Consensus CDS

CCDS93187.1

Related

ENSP00000509117.1, ENST00000684986.1
NM_001410795.1 → NP_001397724.1 myotubularin-related protein 5 isoform 4

Status: REVIEWED

Source sequence(s)

AL096767

Consensus CDS

CCDS93185.1

UniProtKB/TrEMBL

A0A8J8YTQ8

Related

ENSP00000252027.8, ENST00000348911.11
NM_002972.4 → NP_002963.2 myotubularin-related protein 5 isoform 1

See identical proteins and their annotated locations for NP_002963.2

Status: REVIEWED

Source sequence(s)

AL096767, BC087612, BM975530, HY035781

Consensus CDS

CCDS14091.2

UniProtKB/TrEMBL

A0A8I5KVF2

Related

ENSP00000370196.2, ENST00000380817.8

Conserved Domains (8) summary

smart00801
Location:364 → 432

dDENN; Domain always found downstream of DENN domain, found in a variety of signalling proteins

smart00799
Location:129 → 310

DENN; Domain found in a variety of signalling proteins, always encircled by uDENN and dDENN

smart00800
Location:1 → 86

uDENN; Domain always found upstream of DENN domain, found in a variety of signalling proteins

cd01235
Location:1786 → 1891

PH_Sbf1_hMTMR5; Set binding factor 1 (also called Human MTMR5) Pleckstrin Homology (PH) domain

pfam00169
Location:1790 → 1891

PH; PH domain

pfam06602
Location:1128 → 1556

Myotub-related; Myotubularin-like phosphatase domain

pfam12335
Location:543 → 764

SBF2; Myotubularin protein

cl17171
Location:893 → 1011

PH-like; Pleckstrin homology-like domain