SUN3

Sad1 and UNC84 domain containing 3, the group of SUN family

Basic information

Region (hg38): 7:47987148-48029119

Previous symbols: [ "SUNC1" ]

Links

ENSG00000164744 ∙ NCBI:256979 ∙ OMIM:618984 ∙ HGNC:22429 ∙ Uniprot:Q8TAQ9 ∙ 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 SUN3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SUN3 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						0
missense			19	1		20
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	19	1	0

Variants in SUN3

This is a list of pathogenic ClinVar variants found in the SUN3 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-47987448-T-C		not specified	Uncertain significance (Jan 26, 2022)
7-47994329-C-G		not specified	Uncertain significance (Nov 14, 2024)
7-47994347-T-G		not specified	Uncertain significance (Aug 30, 2021)
7-47994362-A-G		not specified	Uncertain significance (Jun 01, 2023)
7-47996054-T-A		not specified	Uncertain significance (Nov 08, 2024)
7-47996077-C-T		not specified	Uncertain significance (Dec 07, 2024)
7-47996116-T-G		not specified	Uncertain significance (Jun 28, 2023)
7-47996122-G-T		not specified	Uncertain significance (Jun 06, 2023)
7-47996133-A-C		not specified	Uncertain significance (May 02, 2024)
7-48005993-C-G		not specified	Uncertain significance (Jun 21, 2022)
7-48007194-C-A		not specified	Uncertain significance (Jan 25, 2023)
7-48007226-A-G		not specified	Likely benign (Mar 25, 2024)
7-48007268-A-G		not specified	Uncertain significance (Jul 05, 2023)
7-48009041-A-C		not specified	Uncertain significance (Oct 28, 2023)
7-48009045-C-T		not specified	Uncertain significance (Dec 21, 2021)
7-48009066-G-A		not specified	Uncertain significance (Feb 01, 2023)
7-48017285-C-T		not specified	Uncertain significance (Mar 08, 2024)
7-48017293-G-A		not specified	Uncertain significance (Oct 05, 2023)
7-48017318-A-G		not specified	Uncertain significance (Jun 16, 2023)
7-48025894-A-G		not specified	Uncertain significance (Aug 19, 2023)
7-48025900-A-G		not specified	Uncertain significance (Nov 03, 2022)
7-48025933-G-C		not specified	Uncertain significance (Jun 21, 2022)
7-48028892-C-T		not specified	Uncertain significance (Jul 26, 2021)
7-48028908-C-T		not specified	Uncertain significance (Mar 18, 2024)
7-48028928-T-C		not specified	Likely benign (Nov 12, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SUN3	protein_coding	protein_coding	ENST00000297325	10	41972

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.00e-12	0.0420	125571	2	175	125748	0.000704

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.518	172	192	0.895	0.00000984	2345
Missense in Polyphen		46	50.459	0.91163		590
Synonymous	0.425	65	69.5	0.935	0.00000396	642
Loss of Function	0.0981	18	18.5	0.975	8.32e-7	251

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000125	0.000124
Ashkenazi Jewish	0.00298	0.00298
East Asian	0.000658	0.000653
Finnish	0.0000471	0.0000462
European (Non-Finnish)	0.000304	0.000299
Middle Eastern	0.000658	0.000653
South Asian	0.00316	0.00308
Other	0.000498	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: As a probable 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. May be involved in nuclear remodeling during sperm head formation in spermatogenenis. A probable SUN3:SYNE1 LINC complex may tether spermatid nuclei to posterior cytoskeletal structures such as the manchette. {ECO:0000250|UniProtKB:Q5SS91}.

Intolerance Scores

• loftool: 0.954
• rvis_EVS: 0.82
• rvis_percentile_EVS: 87.95

Haploinsufficiency Scores

• pHI: 0.144
• hipred: N
• hipred_score: 0.146

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: Sun3

Gene ontology

• Biological process: nuclear envelope organization;cytoskeletal anchoring at nuclear membrane
• Cellular component: nuclear envelope;nuclear inner membrane;integral component of membrane;meiotic nuclear membrane microtubule tethering complex
• Molecular function: protein membrane anchor