CLIP3

CAP-Gly domain containing linker protein 3, the group of Ankyrin repeat domain containing

Basic information

Region (hg38): 19:36014660-36033343

Links

ENSG00000105270

∙ NCBI:25999 ∙ OMIM:607382 ∙ HGNC:24314 ∙ Uniprot:Q96DZ5 ∙ 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 CLIP3 gene.

not_specified (64 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CLIP3 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000015526.3. 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				1 clinvar		1
missense			62 clinvar	1 clinvar		63
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	62	2	0

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CLIP3	protein_coding	protein_coding	ENST00000360535	13	18684

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.679	0.321	125739	0	9	125748	0.0000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.47	176	362	0.486	0.0000252	3515
Missense in Polyphen		42	131.4	0.31962		1188
Synonymous	1.74	133	161	0.826	0.0000125	1147
Loss of Function	3.77	5	25.6	0.195	0.00000133	284

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.000110	0.0000992
East Asian	0.00	0.00
Finnish	0.0000468	0.0000462
European (Non-Finnish)	0.0000558	0.0000527
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: Functions as a cytoplasmic linker protein. Involved in TGN-endosome dynamics. May modulate the cellular compartmentalization of AKT kinase family and promote its cell membrane localization, thereby playing a role in glucose transport in adipocytes. {ECO:0000269|PubMed:19139280}.;
Pathway: Signal Transduction;TNF signaling;Death Receptor Signalling;Regulation of TNFR1 signaling (Consensus)

Recessive Scores

pRec: 0.117

Intolerance Scores

loftool: 0.195
rvis_EVS: -0.74
rvis_percentile_EVS: 13.94

Haploinsufficiency Scores

pHI: 0.308
hipred: Y
hipred_score: 0.662
ghis: 0.663

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: N
gene_indispensability_score: 0.353

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Clip3
Phenotype: muscle phenotype; homeostasis/metabolism phenotype; respiratory system 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); 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);

Gene ontology

Biological process: positive regulation of protein phosphorylation;regulation of tumor necrosis factor-mediated signaling pathway;positive regulation of glucose transmembrane transport;peptidyl-L-cysteine S-palmitoylation;negative regulation of microtubule polymerization;positive regulation of apoptotic process;membrane biogenesis;fat cell differentiation;positive regulation of endocytosis;chaperone-mediated protein transport;positive regulation of protein localization to plasma membrane
Cellular component: Golgi stack;trans-Golgi network;cytosol;plasma membrane;early endosome membrane;trans-Golgi network membrane;membrane raft;recycling endosome membrane
Molecular function: protein binding;microtubule binding;ganglioside binding