CLIP2

CAP-Gly domain containing linker protein 2

Basic information

Region (hg38): 7:74289406-74405935

Previous symbols: [ "WBSCR4", "CYLN2", "WBSCR3" ]

Links

ENSG00000106665 ∙ NCBI:7461 ∙ OMIM:603432 ∙ HGNC:2586 ∙ Uniprot:Q9UDT6 ∙ 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 CLIP2 gene.

• Inborn genetic diseases (37 variants)
• not provided (24 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.

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	11	17
missense			36	3	3	42
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	36	9	14

Variants in CLIP2

This is a list of pathogenic ClinVar variants found in the CLIP2 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-74317581-G-A		not specified	Uncertain significance (Aug 17, 2021)
7-74317586-G-A		not specified	Uncertain significance (Oct 30, 2023)
7-74317638-C-T		not specified	Uncertain significance (Jul 09, 2021)
7-74317644-C-T		not specified	Uncertain significance (Apr 22, 2022)
7-74338451-C-T		not specified	Uncertain significance (Oct 22, 2021)
7-74338482-C-T			Benign (Apr 05, 2018)
7-74338508-C-G		not specified	Uncertain significance (Nov 07, 2022)
7-74338509-C-G			Likely benign (Jan 01, 2023)
7-74338537-G-C		not specified	Uncertain significance (Jan 17, 2024)
7-74338680-C-T			Likely benign (Nov 01, 2023)
7-74338695-G-A			Benign (Apr 05, 2018)
7-74338708-C-A		not specified	Uncertain significance (May 04, 2023)
7-74338708-C-G		not specified	Uncertain significance (Apr 12, 2023)
7-74338738-A-C		not specified	Uncertain significance (Dec 08, 2023)
7-74338771-C-A		not specified	Uncertain significance (Apr 25, 2022)
7-74338803-C-T			Benign (May 01, 2022)
7-74338805-C-G		not specified	Uncertain significance (Dec 09, 2023)
7-74338807-G-A		not specified	Uncertain significance (Feb 12, 2024)
7-74338823-C-T		not specified	Uncertain significance (Dec 27, 2023)
7-74338831-C-T			Benign (May 27, 2017)
7-74338859-C-G		not specified	Uncertain significance (Dec 01, 2022)
7-74338861-C-T			Benign (Oct 01, 2023)
7-74338882-C-T		not specified	Uncertain significance (Dec 13, 2023)
7-74338897-G-A		not specified	Uncertain significance (Aug 12, 2021)
7-74338941-C-A		not specified	Uncertain significance (Feb 23, 2023)

GnomAD

Source: gnomAD

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: dbNSFP

• 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

• Cellular component: microtubule associated complex;cytoplasmic microtubule;microtubule plus-end
• Molecular function: microtubule binding;microtubule plus-end binding