SUN1

Sad1 and UNC84 domain containing 1, the group of SUN family

Basic information

Region (hg38): 7:816614-896435

Previous symbols: [ "UNC84A" ]

Links

ENSG00000164828 ∙ NCBI:23353 ∙ OMIM:607723 ∙ HGNC:18587 ∙ Uniprot:O94901 ∙ 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 SUN1 gene.

• Emery-Dreifuss muscular dystrophy (457 variants)
• not provided (56 variants)
• Inborn genetic diseases (40 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SUN1 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			6	104	10	120
missense			219	10	14	243
nonsense			3			3
start loss						0
frameshift			2			2
inframe indel			1			1
splice donor/acceptor (+/-2bp)			6		1	7
splice region			7	14	7	28
non coding			1	52	52	105
Total	0	0	238	166	77

Variants in SUN1

This is a list of pathogenic ClinVar variants found in the SUN1 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-817715-A-G			Benign (May 16, 2021)
7-832463-T-C			Benign (May 16, 2021)
7-832529-A-C		Emery-Dreifuss muscular dystrophy	Uncertain significance (Aug 27, 2023)
7-832531-T-C		Emery-Dreifuss muscular dystrophy • not specified	Uncertain significance (Jul 21, 2022)
7-832537-C-T		Emery-Dreifuss muscular dystrophy	Uncertain significance (Nov 16, 2023)
7-832538-G-A		Emery-Dreifuss muscular dystrophy	Uncertain significance (Feb 14, 2022)
7-832540-C-A		Emery-Dreifuss muscular dystrophy	Uncertain significance (Jun 27, 2022)
7-832543-C-T		Emery-Dreifuss muscular dystrophy	Uncertain significance (Apr 30, 2022)
7-832547-T-C		Emery-Dreifuss muscular dystrophy • not specified	Conflicting classifications of pathogenicity (Dec 20, 2022)
7-832553-G-A		Emery-Dreifuss muscular dystrophy	Uncertain significance (Dec 16, 2023)
7-832566-T-C		Emery-Dreifuss muscular dystrophy	Likely benign (Aug 22, 2022)
7-832572-G-A		Emery-Dreifuss muscular dystrophy	Likely benign (Nov 15, 2022)
7-832593-T-C		Emery-Dreifuss muscular dystrophy	Likely benign (Oct 13, 2023)
7-832595-C-T		Emery-Dreifuss muscular dystrophy	Uncertain significance (Dec 10, 2023)
7-832596-G-A		Emery-Dreifuss muscular dystrophy	Likely benign (Oct 01, 2022)
7-832600-AG-A		Emery-Dreifuss muscular dystrophy	Uncertain significance (Jul 12, 2022)
7-832602-G-A		Emery-Dreifuss muscular dystrophy	Uncertain significance (Jun 04, 2019)
7-832613-C-T		Emery-Dreifuss muscular dystrophy	Likely benign (Nov 07, 2023)
7-832614-C-T		Emery-Dreifuss muscular dystrophy	Likely benign (Oct 21, 2022)
7-832618-A-T		Emery-Dreifuss muscular dystrophy	Benign (Jan 21, 2024)
7-832619-C-T		Emery-Dreifuss muscular dystrophy	Likely benign (Apr 14, 2023)
7-838779-A-G		Emery-Dreifuss muscular dystrophy	Uncertain significance (Jun 30, 2023)
7-838783-G-A		Emery-Dreifuss muscular dystrophy	Likely benign (Nov 08, 2022)
7-838794-C-T		Emery-Dreifuss muscular dystrophy • SUN1-related disorder	Benign (Jan 22, 2024)
7-838795-T-C		Emery-Dreifuss muscular dystrophy • SUN1-related disorder	Benign (Dec 24, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SUN1	protein_coding	protein_coding	ENST00000401592	19	80545

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000919	1.00	124766	0	48	124814	0.000192

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.331	474	495	0.958	0.0000322	5066
Missense in Polyphen		127	177.48	0.71557		1881
Synonymous	-1.19	246	223	1.10	0.0000171	1569
Loss of Function	3.92	17	45.5	0.374	0.00000240	461

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000612	0.000535
Ashkenazi Jewish	0.00	0.00
East Asian	0.000282	0.000278
Finnish	0.0000934	0.0000928
European (Non-Finnish)	0.000240	0.000229
Middle Eastern	0.000282	0.000278
South Asian	0.000134	0.000131
Other	0.00	0.00

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 (PubMed:18039933, PubMed:18396275). 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 (By similarity). 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 (By similarity). Involved in telomere attachment to nuclear envelope in the prophase of meiosis implicating a SUN1/2:KASH5 LINC complex in which SUN1 and SUN2 seem to act at least partial redundantly (By similarity). Required for gametogenesis and involved in selective gene expression of coding and non-coding RNAs needed for gametogenesis (By similarity). Helps to define the distribution of nuclear pore complexes (NPCs) (By similarity). Required for efficient localization of SYNE4 in the nuclear envelope (By similarity). May be involved in nuclear remodeling during sperm head formation in spermatogenenis (By similarity). May play a role in DNA repair by suppressing non- homologous end joining repair to facilitate the repair of DNA cross-links (PubMed:24375709). {ECO:0000250|UniProtKB:Q9D666, ECO:0000269|PubMed:18039933, ECO:0000269|PubMed:18396275, ECO:0000269|PubMed:24375709}.

Recessive Scores

• pRec: 0.0877

Intolerance Scores

• loftool: 0.725
• rvis_EVS: 0.83
• rvis_percentile_EVS: 88.14

Haploinsufficiency Scores

• pHI: 0.126
• hipred: N
• hipred_score: 0.411
• ghis: 0.500

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sun1
• Phenotype: 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); hearing/vestibular/ear 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); reproductive system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); homeostasis/metabolism phenotype; cellular phenotype; muscle phenotype; endocrine/exocrine gland phenotype; growth/size/body region phenotype

Gene ontology

• Biological process: ossification;nuclear envelope organization;synapsis;spermatogenesis;response to mechanical stimulus;nucleokinesis involved in cell motility in cerebral cortex radial glia guided migration;centrosome localization;meiotic attachment of telomere to nuclear envelope;cytoskeletal anchoring at nuclear membrane;nuclear matrix anchoring at nuclear membrane
• Cellular component: nuclear envelope;integral component of nuclear inner membrane;cytoplasm;nuclear membrane;meiotic nuclear membrane microtubule tethering complex;intracellular membrane-bounded organelle
• Molecular function: protein binding;lamin binding;protein membrane anchor