CASC3

CASC3 exon junction complex subunit, the group of MicroRNA protein coding host genes|Exon junction complex

Basic information

Region (hg38): 17:40140318-40172183

Links

ENSG00000108349 ∙ NCBI:22794 ∙ OMIM:606504 ∙ HGNC:17040 ∙ Uniprot:O15234 ∙ 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 CASC3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CASC3 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			31	3		34
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	31	4	0

Variants in CASC3

This is a list of pathogenic ClinVar variants found in the CASC3 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-40140569-G-C		not specified	Uncertain significance (Aug 04, 2023)
17-40140613-G-C		not specified	Uncertain significance (Dec 28, 2022)
17-40140618-G-C		not specified	Uncertain significance (Aug 04, 2023)
17-40140624-G-A		not specified	Uncertain significance (May 17, 2023)
17-40140723-C-T		not specified	Uncertain significance (Jun 07, 2024)
17-40140747-G-C		not specified	Uncertain significance (Feb 06, 2023)
17-40140769-A-G		not specified	Uncertain significance (Apr 20, 2024)
17-40140772-C-T		not specified	Uncertain significance (Aug 28, 2021)
17-40140775-A-C		not specified	Uncertain significance (Jan 23, 2024)
17-40161817-A-T		not specified	Uncertain significance (Jun 29, 2022)
17-40162087-A-G		not specified	Uncertain significance (Nov 10, 2021)
17-40162736-G-A		not specified	Uncertain significance (Jul 21, 2021)
17-40162804-C-A		not specified	Uncertain significance (Nov 22, 2023)
17-40162856-C-T		not specified	Uncertain significance (Sep 25, 2023)
17-40163542-C-T		not specified	Uncertain significance (Dec 13, 2022)
17-40163550-G-C		not specified	Uncertain significance (Mar 28, 2023)
17-40163592-G-C		not specified	Uncertain significance (Sep 17, 2021)
17-40163678-C-T		not specified	Uncertain significance (Oct 06, 2022)
17-40163680-G-A		not specified	Likely benign (Jun 22, 2023)
17-40163707-C-T		not specified	Uncertain significance (Mar 19, 2024)
17-40163753-G-A		not specified	Uncertain significance (Dec 14, 2022)
17-40163795-A-G		not specified	Uncertain significance (May 08, 2024)
17-40163921-G-A		not specified	Uncertain significance (Oct 16, 2023)
17-40163936-T-C		not specified	Likely benign (Dec 27, 2023)
17-40164011-A-G		not specified	Uncertain significance (Jan 09, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CASC3	protein_coding	protein_coding	ENST00000264645	13	31866

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.613	0.387	125737	0	11	125748	0.0000437

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.32	339	414	0.818	0.0000231	4507
Missense in Polyphen		116	166.86	0.6952		1736
Synonymous	0.548	140	148	0.943	0.00000756	1475
Loss of Function	4.52	8	38.1	0.210	0.00000239	389

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000468	0.0000462
European (Non-Finnish)	0.0000890	0.0000879
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Core component of the splicing-dependent multiprotein exon junction complex (EJC) deposited at splice junctions on mRNAs. The EJC is a dynamic structure consisting of core proteins and several peripheral nuclear and cytoplasmic associated factors that join the complex only transiently either during EJC assembly or during subsequent mRNA metabolism. The EJC marks the position of the exon-exon junction in the mature mRNA for the gene expression machinery and the core components remain bound to spliced mRNAs throughout all stages of mRNA metabolism thereby influencing downstream processes including nuclear mRNA export, subcellular mRNA localization, translation efficiency and nonsense-mediated mRNA decay (NMD). Stimulates the ATPase and RNA- helicase activities of EIF4A3. Plays a role in the stress response by participating in cytoplasmic stress granules assembly and by favoring cell recovery following stress. Component of the dendritic ribonucleoprotein particles (RNPs) in hippocampal neurons. May play a role in mRNA transport. Binds spliced mRNA in sequence-independent manner, 20-24 nucleotides upstream of mRNA exon-exon junctions. Binds poly(G) and poly(U) RNA homopolymer. {ECO:0000269|PubMed:17375189, ECO:0000269|PubMed:17652158}.
• Pathway: mRNA surveillance pathway - Homo sapiens (human);RNA transport - Homo sapiens (human);Gene expression (Transcription);RNA Polymerase II Transcription;Metabolism of RNA;Cleavage of Growing Transcript in the Termination Region ;RNA Polymerase II Transcription Termination;Nonsense-Mediated Decay (NMD);Transport of Mature mRNA derived from an Intron-Containing Transcript;Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC);mRNA 3,-end processing;Transport of Mature Transcript to Cytoplasm;Processing of Capped Intron-Containing Pre-mRNA (Consensus)

Recessive Scores

• pRec: 0.111

Intolerance Scores

• loftool: 0.0981
• rvis_EVS: -0.89
• rvis_percentile_EVS: 10.37

Haploinsufficiency Scores

• pHI: 0.0963
• hipred: Y
• hipred_score: 0.704
• ghis: 0.563

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: E
• gene_indispensability_pred: N
• gene_indispensability_score: 0.307

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Casc3
• Phenotype: embryo 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); limbs/digits/tail phenotype; growth/size/body region phenotype

Gene ontology

• Biological process: nuclear-transcribed mRNA catabolic process, nonsense-mediated decay;mRNA splicing, via spliceosome;RNA export from nucleus;mRNA export from nucleus;regulation of translation;biological_process;intracellular mRNA localization;mRNA 3'-end processing
• Cellular component: nucleoplasm;cytosol;cytoplasmic stress granule;nuclear speck;dendrite;nuclear membrane;exon-exon junction complex;perinuclear region of cytoplasm
• Molecular function: RNA binding;protein binding;enzyme binding;ubiquitin protein ligase binding;identical protein binding