SYNPO synaptopodin [Homo sapiens (human)] - Gene

Summary

Official Symbol: SYNPOprovided by HGNC
Official Full Name: synaptopodinprovided by HGNC
Primary source: HGNC:HGNC:30672
See related: Ensembl:ENSG00000171992 MIM:608155; AllianceGenome:HGNC:30672
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: SYNPO1
Summary: Synaptopodin is an actin-associated protein that may play a role in actin-based cell shape and motility. The name synaptopodin derives from the protein's associations with postsynaptic densities and dendritic spines and with renal podocytes (Mundel et al., 1997 [PubMed 9314539]).[supplied by OMIM, Mar 2008]
Expression: Broad expression in heart (RPKM 65.2), fat (RPKM 35.1) and 20 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 5q33.1

Exon count:: 12

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	5	NC_000005.10 (150586010..150659207)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	5	NC_060929.1 (151122525..151195715)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	5	NC_000005.9 (149980638..150038769)

Chromosome 5 - NC_000005.10 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?

Microbiota-derived butyrate dynamically regulates intestinal homeostasis through regulation of actin-associated protein synaptopodin.
Title: Microbiota-derived butyrate dynamically regulates intestinal homeostasis through regulation of actin-associated protein synaptopodin.
We show that recombinant human KIBRA WW2 domain is primarily disordered, binds SYNPO with relatively weak affinity and remains largely disordered in the complex.
Title: Intrinsic disorder and amino acid specificity modulate binding of the WW2 domain in kidney and brain protein (KIBRA) to synaptopodin.
The postsynaptic protein, synaptopodin (SYNPO) was significantly down-regulated in both dementia with Lewy bodies and Parkinson's disease dementia subgroups, suggesting a defective synaptic transmission in the demented patients.
Title: An iTRAQ-based proteomic analysis reveals dysregulation of neocortical synaptopodin in Lewy body dementias.
Urine synaptopodin is associated with serum creatinine elevation in the patients with glomerulonephritis including diabetic kidney disease regardless of urine albumin excretion. We suggest that the urine synaptopodin level can predict glomerular damage independently of the urine albumin excretion.
Title: Urine synaptopodin excretion is an important marker of glomerular disease progression.
SYNPO variants are involved in AMPA receptor trafficking and neuronal plasticity, which are associated with cognitive impairment and schizophrenia susceptibility.
Title: Exome Sequence Data From Multigenerational Families Implicate AMPA Receptor Trafficking in Neurocognitive Impairment and Schizophrenia Risk.
This study identified and confirmed SYNPO protein changes within the postsynaptic density in schizophrenia
Title: Proteomic and genomic evidence implicates the postsynaptic density in schizophrenia.
Case Report: immunohistologically detected synaptopodin upregulation in foamy podocytes in Fabry disease due to novel alpha-galactosidase A mutation.
Title: A heterozygous female with Fabry disease due to a novel α-galactosidase A mutation exhibits a unique synaptopodin distribution in vacuolated podocytes.
expression significantly down-regulated in presence of WT1 R458Q mutation
Title: A novel missense mutation of Wilms' Tumor 1 causes autosomal dominant FSGS.
Shear stress induced actin binding proteins including SYNPO may play a critical role in endothelial wound healing.
Title: Expression of synaptopodin in endothelial cells exposed to laminar shear stress and its role in endothelial wound healing.
These results suggested that the SA is an important component of the molecular machinery controlling the calcium-dependent accumulation of AMPA-receptors (AMPA-R) at excitatory synapses. [review]
Title: Synaptopodin and the spine apparatus organelle-regulators of different forms of synaptic plasticity?

Submit: New GeneRIF Correction See all GeneRIFs (20)

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

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
Nef	nef	HIV-1 Nef downregulates expression of synaptopodin, a marker for differentiation in podocytes	PubMed
Tat	tat	The gene expression of synaptopodin is significantly upregulated in both clade B and clade C Tat treated SK-N-MC neuroblastoma cells	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

D5S2457 (e-PCR)
- UniSTS:80640

RH47246 (e-PCR)
- UniSTS:78366

SYNPO__5366 (e-PCR)
- UniSTS:463919

D5S470 (e-PCR)
- UniSTS:46914

D5S470 (e-PCR)
- UniSTS:27733

D5S2275E (e-PCR)
- UniSTS:154481

RH16488 (e-PCR)
- UniSTS:48515

SGC34491 (e-PCR)
- UniSTS:69529

SHGC-80801 (e-PCR)
- UniSTS:102323

SHGC-110298 (e-PCR)
- UniSTS:184006

D5S519 (e-PCR)
- UniSTS:147928

D5S1580E (e-PCR)
- UniSTS:151005

WI-17444 (e-PCR)
- UniSTS:47593

D5S640 (e-PCR), detects polymorphism
- UniSTS:31213

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables actin binding	IBA Inferred from Biological aspect of Ancestor more info
enables actin binding	ISS Inferred from Sequence or Structural Similarity more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in modification of dendritic spine	IBA Inferred from Biological aspect of Ancestor more info
involved_in positive regulation of actin filament bundle assembly	IBA Inferred from Biological aspect of Ancestor more info
involved_in positive regulation of actin filament bundle assembly	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of stress fiber assembly	ISS Inferred from Sequence or Structural Similarity more info
involved_in spine apparatus assembly	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
is_active_in Z disc	IBA Inferred from Biological aspect of Ancestor more info
is_active_in actin cytoskeleton	IBA Inferred from Biological aspect of Ancestor more info
located_in actin cytoskeleton	IDA Inferred from Direct Assay more info
located_in actin cytoskeleton	ISS Inferred from Sequence or Structural Similarity more info
located_in bicellular tight junction	IEA Inferred from Electronic Annotation more info
located_in cytosol	IDA Inferred from Direct Assay more info	PubMed
located_in dendritic spine	TAS Traceable Author Statement more info	PubMed
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in perikaryon	IEA Inferred from Electronic Annotation more info
located_in plasma membrane	IDA Inferred from Direct Assay more info
located_in postsynaptic density	IEA Inferred from Electronic Annotation more info
is_active_in spine apparatus	IBA Inferred from Biological aspect of Ancestor more info
is_active_in stress fiber	IBA Inferred from Biological aspect of Ancestor more info

General protein information

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Preferred Names: synaptopodin

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.

mRNA and Protein(s)

NM_001109974.3 → NP_001103444.1 synaptopodin isoform B

See identical proteins and their annotated locations for NP_001103444.1

Status: VALIDATED

Description

Transcript Variant: This variant (2) differs in the 3' coding region and 3' UTR, compared to variant 1. The resulting isoform (B), also referred to as 'Synpo-short', has a distinct C-terminus and is shorter than isoform 1.

Source sequence(s)

AC008453, AL831818, BC146665, DA333058, F30246

Consensus CDS

CCDS54938.1

UniProtKB/Swiss-Prot

Q8N3V7

Related

ENSP00000429268.1, ENST00000519664.1

Conserved Domains (2) summary

PHA03247
Location:269 → 668

PHA03247; large tegument protein UL36; Provisional

PRK13914
Location:15 → 142

PRK13914; invasion associated secreted endopeptidase; Provisional
NM_001166208.2 → NP_001159680.1 synaptopodin isoform C

See identical proteins and their annotated locations for NP_001159680.1

Status: VALIDATED

Description

Transcript Variant: This variant (3) has multiple differences compared to variant 1. These differences result in a distinct 5' UTR and cause translation initiation at an alternate start codon, compared to variant 1. The encoded protein (isoform C) is longer than isoform 1 and contains unique N- and C-termini. Both variants 3 and 4 encode the same isoform (C).

Source sequence(s)

AC008453, AC011383, AK127049, AL831818, F30246

Consensus CDS

CCDS54937.1

UniProtKB/Swiss-Prot

A5PKZ8, D3DQG8, O15271, Q8N3V7, Q9UPX1

UniProtKB/TrEMBL

B3KXB8

Related

ENSP00000377789.1, ENST00000394243.5

Conserved Domains (1) summary

PHA03247
Location:513 → 912

PHA03247; large tegument protein UL36; Provisional
NM_001166209.2 → NP_001159681.1 synaptopodin isoform C

See identical proteins and their annotated locations for NP_001159681.1

Status: VALIDATED

Description

Transcript Variant: This variant (4) has multiple differences compared to variant 1. These differences result in a distinct 5' UTR and cause translation initiation at an alternate start codon, compared to variant 1. The encoded protein (isoform C) is longer than isoform 1 and contains unique N- and C-termini. Both variants 3 and 4 encode the same isoform (C).

Source sequence(s)

AC008453, AK127049, AL831818, F30246

Consensus CDS

CCDS54937.1

UniProtKB/Swiss-Prot

A5PKZ8, D3DQG8, O15271, Q8N3V7, Q9UPX1

UniProtKB/TrEMBL

B3KXB8

Related

ENSP00000428378.1, ENST00000522122.1

Conserved Domains (1) summary

PHA03247
Location:513 → 912

PHA03247; large tegument protein UL36; Provisional
NM_007286.6 → NP_009217.3 synaptopodin isoform A

See identical proteins and their annotated locations for NP_009217.3

Status: VALIDATED

Description

Transcript Variant: This variant (1) represents the longest transcript and encodes isoform A, also referred to as 'Synpo-long'.

Source sequence(s)

AB028952, DA333058

Consensus CDS

CCDS4308.1

UniProtKB/TrEMBL

A7MD96

Related

ENSP00000302139.4, ENST00000307662.5

Conserved Domains (2) summary

cl26464
Location:499 → 900

Atrophin-1; Atrophin-1 family

cl28464
Location:15 → 142

Spr; Cell wall-associated hydrolase, NlpC family [Cell wall/membrane/envelope biogenesis]

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

150586010..150659207

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_047416688.1 → XP_047272644.1 synaptopodin isoform X1

UniProtKB/TrEMBL

B3KXB8
XM_047416689.1 → XP_047272645.1 synaptopodin isoform X1

UniProtKB/TrEMBL

B3KXB8
XM_047416687.1 → XP_047272643.1 synaptopodin isoform X1

UniProtKB/TrEMBL

B3KXB8
XM_006714755.4 → XP_006714818.1 synaptopodin isoform X1

UniProtKB/TrEMBL

B3KXB8

Conserved Domains (2) summary

PHA03247
Location:743 → 1144

PHA03247; large tegument protein UL36; Provisional

PRK13914
Location:259 → 386

PRK13914; invasion associated secreted endopeptidase; Provisional
XM_047416685.1 → XP_047272641.1 synaptopodin isoform X1

UniProtKB/TrEMBL

B3KXB8
XM_047416686.1 → XP_047272642.1 synaptopodin isoform X1

UniProtKB/TrEMBL

B3KXB8
XM_047416684.1 → XP_047272640.1 synaptopodin isoform X1

UniProtKB/TrEMBL

B3KXB8
XM_017009008.2 → XP_016864497.1 synaptopodin isoform X1

UniProtKB/TrEMBL

B3KXB8

Conserved Domains (2) summary

PHA03247
Location:743 → 1144

PHA03247; large tegument protein UL36; Provisional

PRK13914
Location:259 → 386

PRK13914; invasion associated secreted endopeptidase; Provisional
XM_024454351.2 → XP_024310119.2 synaptopodin isoform X3
XM_005268371.2 → XP_005268428.1 synaptopodin isoform X2

See identical proteins and their annotated locations for XP_005268428.1

UniProtKB/TrEMBL

A7MD96

Conserved Domains (2) summary

cl26464
Location:499 → 900

Atrophin-1; Atrophin-1 family

cl28464
Location:15 → 142

Spr; Cell wall-associated hydrolase, NlpC family [Cell wall/membrane/envelope biogenesis]