SUN2

Sad1 and UNC84 domain containing 2, the group of SUN family

Basic information

Region (hg38): 22:38733290-38794143

Previous symbols: [ "UNC84B" ]

Links

ENSG00000100242 ∙ NCBI:25777 ∙ OMIM:613569 ∙ HGNC:14210 ∙ Uniprot:Q9UH99 ∙ 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 SUN2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SUN2 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			2	97	12	111
missense			199	15	11	225
nonsense			4			4
start loss						0
frameshift			2			2
inframe indel			4			4
splice donor/acceptor (+/-2bp)			1			1
splice region			12	12	2	26
non coding			2	33	14	49
Total	0	0	214	145	37

Variants in SUN2

This is a list of pathogenic ClinVar variants found in the SUN2 region.

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

Position	Type	Phenotype	Significance	ClinVar
22-38736270-G-T		Emery-Dreifuss muscular dystrophy	Uncertain significance (Feb 03, 2021)
22-38736274-G-T		Emery-Dreifuss muscular dystrophy	Uncertain significance (May 04, 2022)
22-38736276-G-A		Emery-Dreifuss muscular dystrophy	Likely benign (Nov 19, 2023)
22-38736278-G-A		not specified	Uncertain significance (Mar 28, 2024)
22-38736281-C-T		Emery-Dreifuss muscular dystrophy • not specified	Uncertain significance (Aug 31, 2021)
22-38736299-G-A		Emery-Dreifuss muscular dystrophy	Uncertain significance (May 13, 2022)
22-38736307-C-G		not specified	Uncertain significance (Oct 25, 2022)
22-38736317-C-G		Emery-Dreifuss muscular dystrophy	Uncertain significance (Feb 10, 2022)
22-38736317-C-T		Emery-Dreifuss muscular dystrophy	Uncertain significance (Jul 02, 2022)
22-38736318-G-A		Emery-Dreifuss muscular dystrophy	Likely benign (Mar 18, 2022)
22-38736327-C-G		Emery-Dreifuss muscular dystrophy	Uncertain significance (Oct 13, 2023)
22-38736343-C-A		Emery-Dreifuss muscular dystrophy	Uncertain significance (Dec 03, 2022)
22-38736343-C-T		Emery-Dreifuss muscular dystrophy	Uncertain significance (Jan 03, 2022)
22-38736344-G-A		not specified	Uncertain significance (Aug 15, 2023)
22-38736347-G-A		Emery-Dreifuss muscular dystrophy	Likely benign (Dec 24, 2018)
22-38736348-C-G		Emery-Dreifuss muscular dystrophy	Uncertain significance (Aug 19, 2022)
22-38736363-C-T		Emery-Dreifuss muscular dystrophy	Likely benign (Jul 29, 2023)
22-38736364-G-A		Emery-Dreifuss muscular dystrophy	Uncertain significance (Sep 12, 2023)
22-38736367-GC-G		Emery-Dreifuss muscular dystrophy	Uncertain significance (Mar 14, 2018)
22-38736373-G-A		Emery-Dreifuss muscular dystrophy	Uncertain significance (Jan 20, 2024)
22-38736378-G-C		Emery-Dreifuss muscular dystrophy	Likely benign (Mar 13, 2022)
22-38736378-G-T		Emery-Dreifuss muscular dystrophy	Likely benign (Aug 16, 2022)
22-38736380-C-T		Emery-Dreifuss muscular dystrophy	Uncertain significance (Jun 27, 2022)
22-38736396-A-G		Emery-Dreifuss muscular dystrophy	Likely benign (Apr 10, 2022)
22-38736596-A-T			Benign (May 15, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SUN2	protein_coding	protein_coding	ENST00000405018	17	59419

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.94e-8	1.00	125690	1	57	125748	0.000231

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.945	410	468	0.877	0.0000314	4716
Missense in Polyphen		125	164.42	0.76025		1616
Synonymous	1.53	178	206	0.865	0.0000146	1526
Loss of Function	3.48	21	46.7	0.450	0.00000259	449

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000354	0.000354
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.000910	0.000832
European (Non-Finnish)	0.000162	0.000149
Middle Eastern	0.00	0.00
South Asian	0.000304	0.000261
Other	0.000658	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. Specifically, SYNE2 and SUN2 assemble in arrays of transmembrane actin- associated nuclear (TAN) lines which are bound to F-actin cables and couple the nucleus to retrograde actin flow during actin- dependent nuclear movement. Required for interkinetic nuclear migration (INM) and essential for nucleokinesis and centrosome- nucleus coupling during radial neuronal migration in the cerebral cortex and during glial migration. Required for nuclear migration in retinal photoreceptor progenitors implicating association with cytoplasmic dynein-dynactin and kinesin motor complexes, and probably B-type lamins; SUN1 and SUN2 seem to act redundantly. The SUN1/2:KASH5 LINC complex couples telomeres to microtubules during meiosis; SUN1 and SUN2 seem to act at least partial redundantly. Anchors chromosome movement in the prophase of meiosis and is involved in selective gene expression of coding and non-coding RNAs needed for gametogenesis. Required for telomere attachment to nuclear envelope and gametogenesis. May also function on endocytic vesicles as a receptor for RAB5-GDP and participate in the activation of RAB5. {ECO:0000250|UniProtKB:Q8BJS4, ECO:0000269|PubMed:18396275, ECO:0000305}.

Recessive Scores

• pRec: 0.118

Intolerance Scores

• loftool: 0.897
• rvis_EVS: 0.05
• rvis_percentile_EVS: 57.54

Haploinsufficiency Scores

• pHI: 0.204
• hipred: N
• hipred_score: 0.448
• ghis: 0.497

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.539

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sun2
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); normal phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); homeostasis/metabolism phenotype; cellular phenotype; growth/size/body region phenotype; muscle phenotype

Gene ontology

• Biological process: nuclear envelope organization;mitotic spindle organization;nuclear migration;nucleokinesis involved in cell motility in cerebral cortex radial glia guided migration;positive regulation of cell migration;nuclear migration along microfilament;meiotic cell cycle;centrosome localization;cytoskeletal anchoring at nuclear membrane;nuclear matrix anchoring at nuclear membrane
• Cellular component: nuclear chromosome, telomeric region;condensed nuclear chromosome;nuclear envelope;integral component of nuclear inner membrane;endosome membrane;nuclear membrane;meiotic nuclear membrane microtubule tethering complex
• Molecular function: protein binding;lamin binding;microtubule binding;identical protein binding;protein membrane anchor