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): 14:95407265-95516650

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

Links

ENSG00000176438 ∙ NCBI:161176 ∙ OMIM:610861 ∙ HGNC:19861 ∙ Uniprot:Q6ZMZ3 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

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

• Inborn genetic diseases (61 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.

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.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				1		1
missense			57	4		61
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	57	5	0

Variants in SYNE3

This is a list of pathogenic ClinVar variants found in the SYNE3 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
14-95417863-G-A		not specified	Uncertain significance (Oct 03, 2022)
14-95417872-C-T		not specified	Uncertain significance (Jan 31, 2024)
14-95417888-C-A		not specified	Uncertain significance (Mar 01, 2023)
14-95417899-C-T		not specified	Uncertain significance (Oct 05, 2023)
14-95417993-G-A		not specified	Uncertain significance (Oct 04, 2022)
14-95432095-G-A		not specified	Uncertain significance (Feb 06, 2023)
14-95432096-G-A		not specified	Uncertain significance (Nov 08, 2022)
14-95433310-A-G		not specified	Uncertain significance (Oct 13, 2023)
14-95433326-C-A		not specified	Uncertain significance (Jun 02, 2023)
14-95433349-G-A		not specified	Uncertain significance (May 22, 2023)
14-95433376-G-C		not specified	Uncertain significance (Jun 10, 2022)
14-95433397-G-A		not specified	Uncertain significance (Nov 09, 2021)
14-95436854-G-A		not specified	Uncertain significance (Sep 20, 2023)
14-95436965-T-C		not specified	Uncertain significance (Sep 26, 2023)
14-95439040-C-T		not specified	Uncertain significance (Jun 09, 2022)
14-95439060-C-T		not specified	Uncertain significance (Dec 08, 2023)
14-95439116-T-G		not specified	Uncertain significance (Jan 02, 2024)
14-95439121-G-A		not specified	Uncertain significance (Sep 22, 2023)
14-95439149-A-C		not specified	Uncertain significance (Apr 12, 2023)
14-95439658-C-A		not specified	Uncertain significance (Sep 01, 2021)
14-95439678-T-G		not specified	Uncertain significance (Jun 03, 2022)
14-95439685-C-T		not specified	Uncertain significance (Apr 18, 2023)
14-95439687-G-A		not specified	Uncertain significance (Dec 28, 2023)
14-95439765-G-A		not specified	Uncertain significance (Jan 23, 2023)
14-95439922-C-T		not specified	Uncertain significance (Feb 27, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SYNE3	protein_coding	protein_coding	ENST00000334258	17	58343

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.76e-25	0.00894	125531	0	217	125748	0.000863

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.00387	577	577	1.00	0.0000366	6283
Missense in Polyphen		119	108.82	1.0936		1402
Synonymous	-0.767	274	258	1.06	0.0000167	1983
Loss of Function	1.08	43	51.4	0.837	0.00000254	530

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00294	0.00294
Ashkenazi Jewish	0.00	0.00
East Asian	0.00354	0.00354
Finnish	0.0000950	0.0000924
European (Non-Finnish)	0.000355	0.000352
Middle Eastern	0.00354	0.00354
South Asian	0.000819	0.000817
Other	0.000652	0.000652

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

• 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 Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	High
Cancer	High	Medium	High

Mouse Genome Informatics

• Gene name: Syne3

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