SPART spartin [Homo sapiens (human)] - Gene

Summary

Official Symbol: SPARTprovided by HGNC
Official Full Name: spartinprovided by HGNC
Primary source: HGNC:HGNC:18514
See related: Ensembl:ENSG00000133104 MIM:607111; AllianceGenome:HGNC:18514
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: SPG20; TAHCCP1
Summary: This gene encodes a protein containing a MIT (Microtubule Interacting and Trafficking molecule) domain, and is implicated in regulating endosomal trafficking and mitochondria function. The protein localizes to mitochondria and partially co-localizes with microtubules. Stimulation with epidermal growth factor (EGF) results in protein translocation to the plasma membrane, and the protein functions in the degradation and intracellular trafficking of EGF receptor. Multiple alternatively spliced variants, encoding the same protein, have been identified. Mutations associated with this gene cause autosomal recessive spastic paraplegia 20 (Troyer syndrome). [provided by RefSeq, Nov 2008]
Expression: Ubiquitous expression in ovary (RPKM 20.8), adrenal (RPKM 19.3) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 13q13.3

Exon count:: 15

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	13	NC_000013.11 (36301638..36370180, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	13	NC_060937.1 (35521139..35589682, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	13	NC_000013.10 (36875775..36944317, complement)

Chromosome 13 - NC_000013.11 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
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?

Spastic Paraplegia 20 and Serine/Threonine Protein Kinase 31 Expression for the Detection of Colorectal Cancer.
Title: Spastic Paraplegia 20 and Serine/Threonine Protein Kinase 31 Expression for the Detection of Colorectal Cancer.
KLF4, DAPK1 and SPG20 promoter methylation is not affected by DNMT1 silencing and hypomethylating drugs in lymphoma cells.
Title: KLF4, DAPK1 and SPG20 promoter methylation is not affected by DNMT1 silencing and hypomethylating drugs in lymphoma cells.
The novel mutation in SPART leads to a profound bioenergetic imbalance.
Title: A novel mutation in SPART gene causes a severe neurodevelopmental delay due to mitochondrial dysfunction with complex I impairments and altered pyruvate metabolism.
hypermethylation status of SPG20 gene promoter is significantly associated with intra-hepatic metastasis and contribute to HCC metastasis
Title: Aberrant methylation status of SPG20 promoter in hepatocellular carcinoma: A potential tumor metastasis biomarker.
Methylation-induced Spastic paraplegia 20 silencing facilitates gastric cancer cell proliferation by activating the EGFR/MAPK signaling pathway.
Title: Methylation-induced silencing of SPG20 facilitates gastric cancer cell proliferation by activating the EGFR/MAPK pathway.
we report the clinical findings in three brothers of a consanguineous Moroccan family, aged 24, 17, and 7 yr old, with spastic paraplegia, short stature, motor and cognitive delay, and severe intellectual disability. Targeted exon capture and sequencing showed a homozygous nonsense mutation in the SPG20 gene, c.1369C>T (p.Arg457*), in the three affected boys.
Title: SPG20 mutation in three siblings with familial hereditary spastic paraplegia.
Study identified mutation in SPG20 as the disease causing mutation for Troyer Syndrome in Turkish siblings.
Title: Recurrent null mutation in SPG20 leads to Troyer syndrome.
Up-regulation of SPG20 expression, brought about by trisomy 13 in colon cancer cells trisomy 13 amniocytes, is sufficient for the cytokinesis failure phenotype.
Title: Chromosome mis-segregation and cytokinesis failure in trisomic human cells.
hypermethylation of the spastic paraplegia-20 promoter occurred frequently in gastric cancer.
Title: Detection of aberrant hypermethylated spastic paraplegia-20 as a potential biomarker and prognostic factor in gastric cancer.
The study reveals that hypermethylation in Spastic paraplegia-20 promoter is a highly specific and sensitive biomarker for screening colorectal cancer in stool samples as a noninvasive method.
Title: Detection of hypermethylated spastic paraplegia-20 in stool samples of patients with colorectal cancer.

Submit: New GeneRIF Correction See all GeneRIFs (24)

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
Troyer syndrome MedGen: C0393559 OMIM: 275900 GeneReviews: Troyer 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)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D13S1677 (e-PCR)
- UniSTS:28689

RH45833 (e-PCR)
- UniSTS:7219

RH44628 (e-PCR)
- UniSTS:53047

STS-AA020953 (e-PCR)
- UniSTS:6514

SHGC-53419 (e-PCR)
- UniSTS:65417

SHGC-84682 (e-PCR)
- UniSTS:104083

A009L15 (e-PCR)
- UniSTS:62612

SGC35225 (e-PCR)
- UniSTS:60574

G32643 (e-PCR)
- UniSTS:117226

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables ubiquitin protein ligase binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in BMP signaling pathway	IEA Inferred from Electronic Annotation more info
involved_in abscission	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in adipose tissue development	IEA Inferred from Electronic Annotation more info
involved_in cell division	IBA Inferred from Biological aspect of Ancestor more info
involved_in cell division	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in collateral sprouting in absence of injury	IEA Inferred from Electronic Annotation more info
involved_in lipid droplet organization	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of BMP signaling pathway	IBA Inferred from Biological aspect of Ancestor more info
involved_in negative regulation of collateral sprouting in absence of injury	IEA Inferred from Electronic Annotation more info
involved_in neuromuscular process	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within regulation of mitochondrial membrane potential	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
located_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in cytosol	IDA Inferred from Direct Assay more info
located_in intracellular membrane-bounded organelle	IDA Inferred from Direct Assay more info
located_in lipid droplet	IEA Inferred from Electronic Annotation more info
located_in midbody	IDA Inferred from Direct Assay more info	PubMed
located_in mitochondrial outer membrane	IDA Inferred from Direct Assay more info	PubMed
is_active_in plasma membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in synapse	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: spartin

Names: spastic paraplegia 20 (Troyer syndrome); trans-activated by hepatitis C virus core protein 1

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_011559.2 RefSeqGene

Range

28787..73543

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001142294.2 → NP_001135766.1 spartin

See identical proteins and their annotated locations for NP_001135766.1

Status: REVIEWED

Description

Transcript Variant: This variant (4) differs in the 5' UTR, compared to variant 1. Variants 1, 2, 3, and 4 encode the same protein.

Source sequence(s)

AK057764, AL139377, BC047083, BU622545, DA347686

Consensus CDS

CCDS9356.1

UniProtKB/Swiss-Prot

O60349, Q86Y67, Q8N0X7, Q9H1T2, Q9H1T3

UniProtKB/TrEMBL

A0A024RDV9, A8K6Q9

Related

ENSP00000347314.4, ENST00000355182.8

Conserved Domains (2) summary

cd02679
Location:16 → 95

MIT_spastin; MIT: domain contained within Microtubule Interacting and Trafficking molecules. This MIT domain sub-family is found in the AAA protein spastin, a probable ATPase involved in the assembly or function of nuclear protein complexes; spastins might also be ...

pfam06911
Location:427 → 611

Senescence; Senescence-associated protein
NM_001142295.2 → NP_001135767.1 spartin

See identical proteins and their annotated locations for NP_001135767.1

Status: REVIEWED

Description

Transcript Variant: This variant (3) differs in the 5' UTR, compared to variant 1. Variants 1, 2, 3, and 4 encode the same protein.

Source sequence(s)

AL139377

Consensus CDS

CCDS9356.1

UniProtKB/Swiss-Prot

O60349, Q86Y67, Q8N0X7, Q9H1T2, Q9H1T3

UniProtKB/TrEMBL

A0A024RDV9, A8K6Q9

Related

ENSP00000414147.1, ENST00000451493.5

Conserved Domains (2) summary

cd02679
Location:16 → 95

MIT_spastin; MIT: domain contained within Microtubule Interacting and Trafficking molecules. This MIT domain sub-family is found in the AAA protein spastin, a probable ATPase involved in the assembly or function of nuclear protein complexes; spastins might also be ...

pfam06911
Location:427 → 611

Senescence; Senescence-associated protein
NM_001142296.2 → NP_001135768.1 spartin

See identical proteins and their annotated locations for NP_001135768.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) differs in the 5' UTR, compared to variant 1. Variants 1, 2, 3, and 4 encode the same protein.

Source sequence(s)

AL139377, BC026284, BU622545

Consensus CDS

CCDS9356.1

UniProtKB/Swiss-Prot

O60349, Q86Y67, Q8N0X7, Q9H1T2, Q9H1T3

UniProtKB/TrEMBL

A0A024RDV9, A8K6Q9

Related

ENSP00000473599.1, ENST00000494062.2

Conserved Domains (2) summary

cd02679
Location:16 → 95

MIT_spastin; MIT: domain contained within Microtubule Interacting and Trafficking molecules. This MIT domain sub-family is found in the AAA protein spastin, a probable ATPase involved in the assembly or function of nuclear protein complexes; spastins might also be ...

pfam06911
Location:427 → 611

Senescence; Senescence-associated protein
NM_015087.5 → NP_055902.1 spartin

See identical proteins and their annotated locations for NP_055902.1

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longest transcript. Variants 1, 2, 3, and 4 encode the same protein.

Source sequence(s)

AB011182, AL139377, BU622545, DA710623

Consensus CDS

CCDS9356.1

UniProtKB/Swiss-Prot

O60349, Q86Y67, Q8N0X7, Q9H1T2, Q9H1T3

UniProtKB/TrEMBL

A0A024RDV9, A8K6Q9

Related

ENSP00000406061.2, ENST00000438666.7

Conserved Domains (2) summary

cd02679
Location:16 → 95

MIT_spastin; MIT: domain contained within Microtubule Interacting and Trafficking molecules. This MIT domain sub-family is found in the AAA protein spastin, a probable ATPase involved in the assembly or function of nuclear protein complexes; spastins might also be ...

pfam06911
Location:427 → 611

Senescence; Senescence-associated protein

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000013.11 Reference GRCh38.p14 Primary Assembly

Range

36301638..36370180 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_005266314.4 → XP_005266371.1 spartin isoform X1

See identical proteins and their annotated locations for XP_005266371.1

UniProtKB/Swiss-Prot

O60349, Q86Y67, Q8N0X7, Q9H1T2, Q9H1T3

UniProtKB/TrEMBL

A0A024RDV9, A8K6Q9

Conserved Domains (2) summary

cd02679
Location:16 → 95

MIT_spastin; MIT: domain contained within Microtubule Interacting and Trafficking molecules. This MIT domain sub-family is found in the AAA protein spastin, a probable ATPase involved in the assembly or function of nuclear protein complexes; spastins might also be ...

pfam06911
Location:427 → 611

Senescence; Senescence-associated protein
XM_047430211.1 → XP_047286167.1 spartin isoform X1

UniProtKB/Swiss-Prot

O60349, Q86Y67, Q8N0X7, Q9H1T2, Q9H1T3

UniProtKB/TrEMBL

A0A024RDV9
XM_011535012.3 → XP_011533314.1 spartin isoform X1

See identical proteins and their annotated locations for XP_011533314.1

UniProtKB/Swiss-Prot

O60349, Q86Y67, Q8N0X7, Q9H1T2, Q9H1T3

UniProtKB/TrEMBL

A0A024RDV9, A8K6Q9

Conserved Domains (2) summary

cd02679
Location:16 → 95

MIT_spastin; MIT: domain contained within Microtubule Interacting and Trafficking molecules. This MIT domain sub-family is found in the AAA protein spastin, a probable ATPase involved in the assembly or function of nuclear protein complexes; spastins might also be ...

pfam06911
Location:427 → 611

Senescence; Senescence-associated protein
XM_005266313.6 → XP_005266370.1 spartin isoform X1

See identical proteins and their annotated locations for XP_005266370.1

UniProtKB/Swiss-Prot

O60349, Q86Y67, Q8N0X7, Q9H1T2, Q9H1T3

UniProtKB/TrEMBL

A0A024RDV9, A8K6Q9

Conserved Domains (2) summary

cd02679
Location:16 → 95

MIT_spastin; MIT: domain contained within Microtubule Interacting and Trafficking molecules. This MIT domain sub-family is found in the AAA protein spastin, a probable ATPase involved in the assembly or function of nuclear protein complexes; spastins might also be ...

pfam06911
Location:427 → 611

Senescence; Senescence-associated protein
XM_047430213.1 → XP_047286169.1 spartin isoform X1

UniProtKB/Swiss-Prot

O60349, Q86Y67, Q8N0X7, Q9H1T2, Q9H1T3

UniProtKB/TrEMBL

A0A024RDV9
XM_024449334.2 → XP_024305102.1 spartin isoform X1

UniProtKB/Swiss-Prot

O60349, Q86Y67, Q8N0X7, Q9H1T2, Q9H1T3

UniProtKB/TrEMBL

A0A024RDV9, A8K6Q9

Conserved Domains (2) summary

cd02679
Location:16 → 95

MIT_spastin; MIT: domain contained within Microtubule Interacting and Trafficking molecules. This MIT domain sub-family is found in the AAA protein spastin, a probable ATPase involved in the assembly or function of nuclear protein complexes; spastins might also be ...

pfam06911
Location:427 → 611

Senescence; Senescence-associated protein
XM_047430210.1 → XP_047286166.1 spartin isoform X1

UniProtKB/Swiss-Prot

O60349, Q86Y67, Q8N0X7, Q9H1T2, Q9H1T3

UniProtKB/TrEMBL

A0A024RDV9
XM_005266317.4 → XP_005266374.1 spartin isoform X1

See identical proteins and their annotated locations for XP_005266374.1

UniProtKB/Swiss-Prot

O60349, Q86Y67, Q8N0X7, Q9H1T2, Q9H1T3

UniProtKB/TrEMBL

A0A024RDV9, A8K6Q9

Conserved Domains (2) summary

cd02679
Location:16 → 95

MIT_spastin; MIT: domain contained within Microtubule Interacting and Trafficking molecules. This MIT domain sub-family is found in the AAA protein spastin, a probable ATPase involved in the assembly or function of nuclear protein complexes; spastins might also be ...

pfam06911
Location:427 → 611

Senescence; Senescence-associated protein
XM_005266315.4 → XP_005266372.1 spartin isoform X1

See identical proteins and their annotated locations for XP_005266372.1

UniProtKB/Swiss-Prot

O60349, Q86Y67, Q8N0X7, Q9H1T2, Q9H1T3

UniProtKB/TrEMBL

A0A024RDV9, A8K6Q9

Conserved Domains (2) summary

cd02679
Location:16 → 95

MIT_spastin; MIT: domain contained within Microtubule Interacting and Trafficking molecules. This MIT domain sub-family is found in the AAA protein spastin, a probable ATPase involved in the assembly or function of nuclear protein complexes; spastins might also be ...

pfam06911
Location:427 → 611

Senescence; Senescence-associated protein
XM_047430209.1 → XP_047286165.1 spartin isoform X1

UniProtKB/Swiss-Prot

O60349, Q86Y67, Q8N0X7, Q9H1T2, Q9H1T3

UniProtKB/TrEMBL

A0A024RDV9
XM_047430212.1 → XP_047286168.1 spartin isoform X1

UniProtKB/Swiss-Prot

O60349, Q86Y67, Q8N0X7, Q9H1T2, Q9H1T3

UniProtKB/TrEMBL

A0A024RDV9