SYNE3 spectrin repeat containing nuclear envelope family member 3 [Homo sapiens (human)] - Gene

Summary

Official Symbol: SYNE3provided by HGNC
Official Full Name: spectrin repeat containing nuclear envelope family member 3provided by HGNC
Primary source: HGNC:HGNC:19861
See related: Ensembl:ENSG00000176438 MIM:610861; AllianceGenome:HGNC:19861
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: KASH3; NET53; Nesp3; C14orf49; C14orf139; LINC00341; NCRNA00341
Summary: Enables actin filament binding activity and cytoskeleton-nuclear membrane anchor activity. Involved in cytoskeleton organization; establishment of protein localization to membrane; and regulation of cell shape. Located in nuclear membrane. Part of meiotic nuclear membrane microtubule tethering complex. Biomarker of Huntington's disease. [provided by Alliance of Genome Resources, Apr 2022]
Expression: Ubiquitous expression in fat (RPKM 4.3), bone marrow (RPKM 3.9) and 24 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 14q32.13

Exon count:: 21

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	14	NC_000014.9 (95407266..95516650, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	14	NC_060938.1 (89637225..89747355, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	14	NC_000014.8 (95873603..95982987, complement)

Chromosome 14 - NC_000014.9 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

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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?

Expression profile of SYNE3 and bioinformatic analysis of its prognostic value and functions in tumors.
Title: Expression profile of SYNE3 and bioinformatic analysis of its prognostic value and functions in tumors.
Structural Analysis of Different LINC Complexes Reveals Distinct Binding Modes.
Title: Structural Analysis of Different LINC Complexes Reveals Distinct Binding Modes.
Long Noncoding RNAs as Bone Marrow Stem Cell Regulators in Osteoporosis.
Title: Long Noncoding RNAs as Bone Marrow Stem Cell Regulators in Osteoporosis.
LINC00341 interacts with miR-141 to suppress its functional binding to the 3'-untranslated region of YAF2 messenger RNA whereby supporting chondrocyte survival and preventing osteoarthritis progression.
Title: A LINC00341-mediated regulatory pathway supports chondrocyte survival and may prevent osteoarthritis progression.
SPAG4, in cooperation with Nesprin3, has a fundamental pathological function in the migration of lung carcinoma cells.
Title: Sperm‑associated antigen 4 (SPAG4) as a new cancer marker interacts with Nesprin3 to regulate cell migration in lung carcinoma.
Overexpression of LINC00341 suppresses the expression of vascular cell adhesion molecule 1 (VCAM1) and the adhesion of monocytes induced by atheroprone flow and tumor necrosis factor-alpha.
Title: LINC00341 exerts an anti-inflammatory effect on endothelial cells by repressing VCAM1.
Meta-analysis estimated the relationship between LINC00341 expression and distant metastasis or lymph node metastasis in breast cancer.
Title: Relationship between LINC00341 expression and cancer prognosis.
nesprin-3 regulates vascular endothelial cell shape, perinuclear cytoskeletal architecture, and important aspects of flow-mediated mechanotransduction.
Title: Nesprin-3 regulates endothelial cell morphology, perinuclear cytoskeletal architecture, and flow-induced polarization.
association with human nesprin-3 appeared to be stronger for torsinADeltaE than for torsinA. TorsinA also associated with the KASH domains of nesprin-1 and -2
Title: TorsinA binds the KASH domain of nesprins and participates in linkage between nuclear envelope and cytoskeleton.

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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
A genome-wide association study of survival in small-cell lung cancer patients treated with irinotecan plus cisplatin chemotherapy. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study of sex hormones, gonadotropins and sex hormone-binding protein in Chinese men. 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

SHGC-144584 (e-PCR)
- UniSTS:182790

RH92376 (e-PCR)
- UniSTS:83816

G63168 (e-PCR)
- UniSTS:140285

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables actin filament binding	IBA Inferred from Biological aspect of Ancestor more info
enables actin filament binding	IMP Inferred from Mutant Phenotype more info	PubMed
enables cytoskeleton-nuclear membrane anchor activity	IDA Inferred from Direct Assay more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in cytoskeleton organization	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in establishment of protein localization to membrane	IDA Inferred from Direct Assay more info	PubMed
involved_in nuclear migration	IBA Inferred from Biological aspect of Ancestor more info
involved_in regulation of cell shape	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
is_active_in cytoplasm	IBA Inferred from Biological aspect of Ancestor more info
part_of meiotic nuclear membrane microtubule tethering complex	IBA Inferred from Biological aspect of Ancestor more info
part_of meiotic nuclear membrane microtubule tethering complex	IDA Inferred from Direct Assay more info	PubMed
located_in membrane	HDA more info	PubMed
located_in nuclear envelope	IDA Inferred from Direct Assay more info	PubMed
located_in nuclear membrane	IDA Inferred from Direct Assay more info
is_active_in nuclear outer membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in rough endoplasmic reticulum	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: nesprin-3

Names: KASH domain-containing protein 3; long intergenic non-protein coding RNA 341; nuclear envelope spectrin repeat protein 3; uncharacterized protein C14orf113

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_001363692.2 → NP_001350621.1 nesprin-3 isoform 2

Status: VALIDATED

Source sequence(s)

AL133467, AL138539

Consensus CDS

CCDS86430.1

Related

ENSP00000450562.1, ENST00000557275.5

Conserved Domains (3) summary

pfam10541
Location:941 → 970

KASH; Nuclear envelope localization domain

cl02488
Location:562 → 739

SPEC; Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; ...

cl25732
Location:141 → 760

SMC_N; RecF/RecN/SMC N terminal domain
NM_001384281.1 → NP_001371210.1 nesprin-3 isoform 3

Status: VALIDATED

Source sequence(s)

AL133467, AL138539

Consensus CDS

CCDS91927.1

Related

ENSP00000450774.1, ENST00000553340.1

Conserved Domains (1) summary

TIGR02168
Location:156 → 427

SMC_prok_B; chromosome segregation protein SMC, common bacterial type
NM_001384282.1 → NP_001371211.1 nesprin-3 isoform 3

Status: VALIDATED

Source sequence(s)

AL133467, AL138539

Consensus CDS

CCDS91927.1

Conserved Domains (1) summary

TIGR02168
Location:156 → 427

SMC_prok_B; chromosome segregation protein SMC, common bacterial type
NM_001384283.1 → NP_001371212.1 nesprin-3 isoform 4

Status: VALIDATED

Source sequence(s)

AL133467, AL138539

Conserved Domains (1) summary

TIGR02168
Location:164 → 435

SMC_prok_B; chromosome segregation protein SMC, common bacterial type
NM_001384284.1 → NP_001371213.1 nesprin-3 isoform 5

Status: VALIDATED

Source sequence(s)

AL133467, AL138539

Conserved Domains (1) summary

TIGR02168
Location:156 → 427

SMC_prok_B; chromosome segregation protein SMC, common bacterial type
NM_152592.6 → NP_689805.3 nesprin-3 isoform 1

See identical proteins and their annotated locations for NP_689805.3

Status: VALIDATED

Source sequence(s)

AL133467, AL138539

Consensus CDS

CCDS9935.1

UniProtKB/Swiss-Prot

A6H8H3, Q6ZMZ3, Q86SX5, Q8N7G8

Related

ENSP00000507501.1, ENST00000682763.1

Conserved Domains (3) summary

TIGR02168
Location:141 → 760

SMC_prok_B; chromosome segregation protein SMC, common bacterial type

pfam10541
Location:946 → 975

KASH; Nuclear envelope localization domain

cl02488
Location:562 → 739

SPEC; Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; ...

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_000014.9 Reference GRCh38.p14 Primary Assembly

Range

95407266..95516650 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

NC_060938.1 Alternate T2T-CHM13v2.0

Range

89637225..89747355 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

NM_024633.2: Suppressed sequence

Description

NM_024633.2: This RefSeq was permanently suppressed because currently there is support for the transcript but not for the protein.