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.

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.

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			42			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	42	0	0

Variants in CLIP3

This is a list of pathogenic ClinVar variants found in the CLIP3 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-36016964-C-T		not specified	Uncertain significance (May 03, 2023)
19-36017416-C-T		not specified	Uncertain significance (Jun 02, 2023)
19-36017425-C-T		not specified	Uncertain significance (Dec 06, 2022)
19-36017450-C-T		not specified	Likely benign (Oct 20, 2024)
19-36017691-C-G		not specified	Uncertain significance (Apr 15, 2024)
19-36017869-C-T		not specified	Uncertain significance (Sep 06, 2022)
19-36017877-C-T		not specified	Uncertain significance (Sep 16, 2021)
19-36017938-C-T		not specified	Uncertain significance (Mar 01, 2024)
19-36017943-C-T		not specified	Uncertain significance (May 24, 2023)
19-36017970-G-A		not specified	Uncertain significance (Sep 12, 2024)
19-36018912-C-T		not specified	Uncertain significance (Dec 05, 2022)
19-36018915-C-G		not specified	Uncertain significance (Dec 08, 2023)
19-36018922-C-T		not specified	Uncertain significance (Jan 03, 2022)
19-36018931-G-A		not specified	Uncertain significance (Jul 11, 2023)
19-36018938-G-C		not specified	Uncertain significance (May 03, 2023)
19-36019173-T-C		not specified	Uncertain significance (Nov 08, 2022)
19-36024430-C-T		not specified	Uncertain significance (Jan 10, 2022)
19-36024452-T-G		not specified	Uncertain significance (Sep 06, 2024)
19-36024467-C-T		not specified	Uncertain significance (Feb 12, 2024)
19-36024493-T-C		not specified	Uncertain significance (May 23, 2024)
19-36024503-C-T		not specified	Uncertain significance (Sep 30, 2024)
19-36024518-C-T		not specified	Uncertain significance (Apr 26, 2024)
19-36024535-G-A		not specified	Uncertain significance (Jul 08, 2022)
19-36024539-G-A		not specified	Uncertain significance (Jan 23, 2024)
19-36024562-G-A		not specified	Uncertain significance (Sep 09, 2021)

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