CLIP1

CAP-Gly domain containing linker protein 1

Basic information

Region (hg38): 12:122271432-122422669

Previous symbols: [ "RSN" ]

Links

ENSG00000130779

∙ NCBI:6249 ∙ OMIM:179838 ∙ HGNC:10461 ∙ Uniprot:P30622 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

autosomal recessive non-syndromic intellectual disability (Supportive), mode of inheritance: AR
intellectual disability (Limited), mode of inheritance: AR

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CLIP1 gene.

not_specified (166 variants)
not_provided (27 variants)
CLIP1-related_disorder (7 variants)
CLIP1-related_intellectual_disability (3 variants)
EBV-positive_nodal_T-_and_NK-cell_lymphoma (1 variants)
Short_stature (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CLIP1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001247997.2. 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			3 clinvar	22 clinvar	6 clinvar	31
missense			147 clinvar	9 clinvar		156
nonsense	1 clinvar		1 clinvar			2
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	1	0	153	31	6

Highest pathogenic variant AF is 0.00000371813

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CLIP1	protein_coding	protein_coding	ENST00000540338	25	151201

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.681	0.319	125606	0	142	125748	0.000565

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.08	589	749	0.787	0.0000409	9488
Missense in Polyphen		313	442.01	0.70813		5691
Synonymous	-0.944	314	293	1.07	0.0000176	2650
Loss of Function	6.07	15	69.7	0.215	0.00000356	920

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000847	0.000846
Ashkenazi Jewish	0.00253	0.00199
East Asian	0.000330	0.000326
Finnish	0.000143	0.000139
European (Non-Finnish)	0.000572	0.000545
Middle Eastern	0.000330	0.000326
South Asian	0.000944	0.000752
Other	0.00126	0.00114

dbNSFP

Source: dbNSFP

Function: FUNCTION: Binds to the plus end of microtubules and regulates the dynamics of the microtubule cytoskeleton. Promotes microtubule growth and microtubule bundling. Links cytoplasmic vesicles to microtubules and thereby plays an important role in intracellular vesicle trafficking. Plays a role macropinocytosis and endosome trafficking. {ECO:0000269|PubMed:12433698, ECO:0000269|PubMed:17563362, ECO:0000269|PubMed:17889670}.;
Pathway: mTOR signaling pathway - Homo sapiens (human);Regulation of Microtubule Cytoskeleton;Signal Transduction;lissencephaly gene (lis1) in neuronal migration and development;Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal;Amplification of signal from the kinetochores;Mitotic Spindle Checkpoint;Cell Cycle Checkpoints;RHO GTPases Activate Formins;RHO GTPases activate IQGAPs;RHO GTPase Effectors;Signaling by Rho GTPases;Mitotic Prometaphase;Separation of Sister Chromatids;Mitotic Anaphase;Mitotic Metaphase and Anaphase;M Phase;Cell Cycle;Resolution of Sister Chromatid Cohesion;Cell Cycle, Mitotic;mTOR signaling pathway;Lissencephaly gene (LIS1) in neuronal migration and development (Consensus)

Recessive Scores

pRec: 0.323

Intolerance Scores

loftool: 0.729
rvis_EVS: -1.1
rvis_percentile_EVS: 6.95

Haploinsufficiency Scores

pHI: 0.467
hipred: Y
hipred_score: 0.718
ghis: 0.628

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.797

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	High	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High

Mouse Genome Informatics

Gene name: Clip1
Phenotype: cellular phenotype; reproductive system phenotype;

Zebrafish Information Network

Gene name: clip1a
Affected structure: epiboly involved in gastrulation with mouth forming second
Phenotype tag: abnormal
Phenotype quality: delayed

Gene ontology

Biological process: mitotic cell cycle;microtubule bundle formation;positive regulation of microtubule polymerization;protein transport into plasma membrane raft
Cellular component: kinetochore;ruffle;nuclear envelope;endosome;centrosome;cytosol;microtubule;cytoplasmic microtubule;intermediate filament;microtubule cytoskeleton;cytoplasmic vesicle membrane;microtubule plus-end;macropinosome
Molecular function: protein binding;microtubule binding;zinc ion binding;tubulin binding;protein homodimerization activity;metal ion binding;microtubule plus-end binding