CLIP2
Basic information
Region (hg38): 7:74289407-74405935
Previous symbols: [ "WBSCR4", "CYLN2", "WBSCR3" ]
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (121 variants)
- not_provided (33 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the CLIP2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000003388.5. Only rare variants are included in the table.
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.
Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
---|---|---|---|---|---|---|
synonymous | 10 | 11 | 21 | |||
missense | 116 | 128 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 1 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
Total | 0 | 0 | 117 | 19 | 14 |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
CLIP2 | protein_coding | protein_coding | ENST00000223398 | 16 | 116469 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
1.00 | 0.0000340 | 125734 | 0 | 14 | 125748 | 0.0000557 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 2.36 | 493 | 664 | 0.743 | 0.0000464 | 6629 |
Missense in Polyphen | 116 | 223.76 | 0.51842 | 2271 | ||
Synonymous | -0.701 | 338 | 322 | 1.05 | 0.0000244 | 2161 |
Loss of Function | 5.79 | 4 | 46.7 | 0.0857 | 0.00000235 | 535 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.0000624 | 0.0000615 |
Ashkenazi Jewish | 0.000102 | 0.0000992 |
East Asian | 0.0000557 | 0.0000544 |
Finnish | 0.000102 | 0.0000924 |
European (Non-Finnish) | 0.0000542 | 0.0000527 |
Middle Eastern | 0.0000557 | 0.0000544 |
South Asian | 0.0000982 | 0.0000980 |
Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Seems to link microtubules to dendritic lamellar body (DLB), a membranous organelle predominantly present in bulbous dendritic appendages of neurons linked by dendrodendritic gap junctions. May operate in the control of brain-specific organelle translocations (By similarity). {ECO:0000250}.;
- Disease
- DISEASE: Note=CLIP2 is located in the Williams-Beuren syndrome (WBS) critical region (PubMed:9799601). WBS results from a hemizygous deletion of several genes on chromosome 7q11.23, thought to arise as a consequence of unequal crossing over between highly homologous low-copy repeat sequences flanking the deleted region. Haploinsufficiency of CLIP2 may be the cause of certain cardiovascular and musculo-skeletal abnormalities observed in the disease. However, it has been demonstrated that haploinsufficiency of this gene alone is not sufficient to cause any of the cognitive or facial features of WBS (PubMed:22608712). {ECO:0000305|PubMed:22608712, ECO:0000305|PubMed:9799601}.;
Intolerance Scores
- loftool
- 0.127
- rvis_EVS
- -1.19
- rvis_percentile_EVS
- 5.9
Haploinsufficiency Scores
- pHI
- 0.131
- hipred
- Y
- hipred_score
- 0.728
- ghis
- 0.528
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.838
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Clip2
- Phenotype
- skeleton 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); normal phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); cellular phenotype; growth/size/body region phenotype;
Gene ontology
- Biological process
- Cellular component
- microtubule associated complex;cytoplasmic microtubule;microtubule plus-end
- Molecular function
- microtubule binding;microtubule plus-end binding