SYNPO2L synaptopodin 2 like [Homo sapiens (human)] - Gene

Summary

Official Symbol: SYNPO2Lprovided by HGNC
Official Full Name: synaptopodin 2 likeprovided by HGNC
Primary source: HGNC:HGNC:23532
See related: Ensembl:ENSG00000166317 AllianceGenome:HGNC:23532
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
Summary: Predicted to enable actin binding activity. Predicted to be involved in several processes, including positive regulation of Rho protein signal transduction; positive regulation of stress fiber assembly; and sarcomere organization. Predicted to be located in cytoplasm and cytoskeleton. Predicted to be active in Z disc; actin cytoskeleton; and nucleus. [provided by Alliance of Genome Resources, Dec 2024]
Expression: Restricted expression toward heart (RPKM 82.2) See more
Orthologs: mouse all
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Genomic context

Location:: 10q22.2

Exon count:: 5

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	10	NC_000010.11 (73644886..73656029, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	10	NC_060934.1 (74516308..74527453, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	10	NC_000010.10 (75404644..75415787, complement)

Chromosome 10 - NC_000010.11 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?

METTL16 Promotes Stability of SYNPO2L mRNA and leading to Cancer Cell Lung Metastasis by Secretion of COL10A1 and attract the Cancer-Associated Fibroblasts.
Title: METTL16 Promotes Stability of SYNPO2L mRNA and leading to Cancer Cell Lung Metastasis by Secretion of COL10A1 and attract the Cancer-Associated Fibroblasts.
we did not observe associations between coding genetic variants and Atrial fibrillation (AF), suggesting that large-effect coding variation is not the predominant mechanism underlying AF. A coding variant in SYNPO2L requires further evaluation to determine whether it is causally related to AF
Title: Whole Exome Sequencing in Atrial Fibrillation.
Observational study of gene-disease association. (HuGE Navigator)
Title: A scan of chromosome 10 identifies a novel locus showing strong association with late-onset Alzheimer disease.

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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
Meta-analysis identifies six new susceptibility loci for atrial fibrillation. 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

D11S2921 (e-PCR)
- UniSTS:152074

D10S283 (e-PCR)
- UniSTS:148005

D10S1313E (e-PCR)
- UniSTS:151345

sY3084 (e-PCR)
- UniSTS:515126

D10S188 (e-PCR), detects polymorphism
- UniSTS:48962

MARC_17634-17635:1019143787:1 (e-PCR)
- UniSTS:268361

D10S463 (e-PCR)
- UniSTS:148059

D10S188 (e-PCR), detects polymorphism
- UniSTS:70051

RH102916 (e-PCR)
- UniSTS:97250

Gene Ontology Provided by GOA

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

Process	Evidence Code	Pubs
involved_in heart morphogenesis	ISS Inferred from Sequence or Structural Similarity more info	PubMed
involved_in positive regulation of Rho protein signal transduction	ISS Inferred from Sequence or Structural Similarity more info	PubMed
involved_in positive regulation of actin filament bundle assembly	IBA Inferred from Biological aspect of Ancestor more info
involved_in positive regulation of stress fiber assembly	ISS Inferred from Sequence or Structural Similarity more info	PubMed
involved_in sarcomere organization	ISS Inferred from Sequence or Structural Similarity more info	PubMed

Component	Evidence Code	Pubs
is_active_in Z disc	IBA Inferred from Biological aspect of Ancestor more info
located_in Z disc	ISS Inferred from Sequence or Structural Similarity more info	PubMed
is_active_in actin cytoskeleton	IBA Inferred from Biological aspect of Ancestor more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info

General protein information

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Preferred Names: synaptopodin 2-like protein

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_001114133.3 → NP_001107605.1 synaptopodin 2-like protein isoform a

See identical proteins and their annotated locations for NP_001107605.1

Status: VALIDATED

Description

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

Source sequence(s)

AB188489, AK022983

Consensus CDS

CCDS44438.1

UniProtKB/Swiss-Prot

A5PKV9, Q68A20, Q9H987

UniProtKB/TrEMBL

B4DJ09

Related

ENSP00000378289.2, ENST00000394810.3

Conserved Domains (1) summary

cd00992
Location:6 → 85

PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...
NM_024875.5 → NP_079151.2 synaptopodin 2-like protein isoform b

See identical proteins and their annotated locations for NP_079151.2

Status: VALIDATED

Description

Transcript Variant: This variant (2) contains an alternate 5' terminal exon resulting in different 5' UTR and 5' coding regions, compared to variant 1. It encodes isoform b, which is shorter and has a distinct N-terminus, compared to isoform a.

Source sequence(s)

AB188489, AC073389, AK022983, BC142635, DA685385

Consensus CDS

CCDS7331.1

Related

ENSP00000361964.4, ENST00000372873.8

Conserved Domains (1) summary

cl26247
Location:191 → 326

DNA_pol3_delta2; DNA polymerase III, delta subunit