SYNE3

spectrin repeat containing nuclear envelope family member 3, the group of KASH domain containing|Spectrin repeat containing nuclear envelope family

Basic information

Region (hg38): 14:95407266-95516650

Previous symbols: [ "C14orf49", "LINC00341", "C14orf139", "NCRNA00341" ]

Links

ENSG00000176438NCBI:161176OMIM:610861HGNC:19861Uniprot:Q6ZMZ3AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SYNE3 gene.

  • not_specified (170 variants)
  • not_provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SYNE3 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000152592.6. Only rare variants are included in the table.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

EffectPLPVUSLBBSum
synonymous
1
clinvar
1
missense
158
clinvar
12
clinvar
170
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
0
Total 0 0 158 13 0
Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
SYNE3protein_codingprotein_codingENST00000334258 1758343
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
1.76e-250.0089412553102171257480.000863
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense-0.003875775771.000.00003666283
Missense in Polyphen119108.821.09361402
Synonymous-0.7672742581.060.00001671983
Loss of Function1.084351.40.8370.00000254530

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.002940.00294
Ashkenazi Jewish0.000.00
East Asian0.003540.00354
Finnish0.00009500.0000924
European (Non-Finnish)0.0003550.000352
Middle Eastern0.003540.00354
South Asian0.0008190.000817
Other0.0006520.000652

dbNSFP

Source: dbNSFP

Function
FUNCTION: As a component of the LINC (LInker of Nucleoskeleton and Cytoskeleton) complex involved in the connection between the nuclear lamina and the cytoskeleton. The nucleocytoplasmic interactions established by the LINC complex play an important role in the transmission of mechanical forces across the nuclear envelope and in nuclear movement and positioning. Probable anchoring protein which tethers the nucleus to the cytoskeleton by binding PLEC which can associate with the intermediate filament system. Plays a role in the regulation of aortic epithelial cell morphology, and is required for flow-induced centrosome polarization and directional migration in aortic endothelial cells. {ECO:0000269|PubMed:16330710, ECO:0000269|PubMed:18396275, ECO:0000269|PubMed:21937718}.;

Recessive Scores

pRec
0.106

Intolerance Scores

loftool
rvis_EVS
1.17
rvis_percentile_EVS
92.66

Haploinsufficiency Scores

pHI
0.123
hipred
N
hipred_score
0.144
ghis
0.448

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
gene_indispensability_score

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumHigh
CancerHighMediumHigh

Mouse Genome Informatics

Gene name
Syne3
Phenotype

Zebrafish Information Network

Gene name
syne3
Affected structure
epidermal cell
Phenotype tag
abnormal
Phenotype quality
spatial pattern

Gene ontology

Biological process
cytoskeleton organization;nuclear migration;regulation of cell shape;nucleus localization;establishment of protein localization to membrane;cytoskeletal anchoring at nuclear membrane
Cellular component
nuclear envelope;nuclear outer membrane;cytoplasm;rough endoplasmic reticulum;membrane;integral component of membrane;nuclear membrane;meiotic nuclear membrane microtubule tethering complex
Molecular function
protein binding;actin filament binding