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GeneBe

CLIP1

CAP-Gly domain containing linker protein 1

Basic information

Region (hg38): 12:122271431-122422669

Previous symbols: [ "RSN" ]

Links

ENSG00000130779NCBI:6249OMIM:179838HGNC:10461Uniprot:P30622AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

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.

  • Inborn genetic diseases (42 variants)
  • not specified (26 variants)
  • not provided (25 variants)
  • CLIP1-related intellectual disability (2 variants)
  • Global developmental delay (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.

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
3
clinvar
16
clinvar
5
clinvar
24
missense
53
clinvar
3
clinvar
56
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
1
clinvar
1
splice region
?
0
non coding
?
1
clinvar
1
clinvar
1
clinvar
3
Total 0 0 58 20 6

Variants in CLIP1

This is a list of pathogenic ClinVar variants found in the CLIP1 region.

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

Position Type Phenotype Significance ClinVar
12-122272929-G-C Inborn genetic diseases Uncertain significance (Aug 12, 2021)2244334
12-122272966-T-C not specified Uncertain significance (Dec 30, 2016)434774
12-122273011-G-C Inborn genetic diseases Uncertain significance (Aug 01, 2022)2304324
12-122273074-T-C Global developmental delay Uncertain significance (Jan 16, 2020)978177
12-122274063-C-T not specified • Inborn genetic diseases Uncertain significance (Nov 15, 2021)434775
12-122274122-T-C Inborn genetic diseases Uncertain significance (Jun 22, 2023)2605203
12-122274172-T-TA not specified Benign (Sep 23, 2019)1336261
12-122278196-T-C Benign (Dec 05, 2017)717357
12-122278783-G-A Likely benign (May 25, 2018)745583
12-122278800-C-G Inborn genetic diseases Uncertain significance (Sep 16, 2021)2400912
12-122278859-G-C Likely benign (Dec 31, 2019)749337
12-122278880-T-C not specified Likely benign (Jul 21, 2016)434776
12-122278908-T-C CLIP1-related intellectual disability • Inborn genetic diseases Uncertain significance (Apr 12, 2022)1696622
12-122279084-T-A not specified Uncertain significance (Mar 06, 2018)1336583
12-122279123-C-A Likely benign (Dec 31, 2019)788442
12-122309789-G-A Likely benign (Oct 01, 2022)2643497
12-122316808-G-C not specified Uncertain significance (Feb 28, 2020)1337549
12-122319262-G-A not specified Likely benign (Jun 21, 2018)1336241
12-122319334-C-T Likely benign (Dec 11, 2017)733921
12-122319343-A-G Likely benign (Dec 31, 2019)791365
12-122327937-C-T not specified Uncertain significance (Aug 29, 2016)434777
12-122328016-G-A Benign (Dec 31, 2019)721639
12-122328047-G-A Inborn genetic diseases Likely benign (May 23, 2023)2550092
12-122328083-G-C Inborn genetic diseases Uncertain significance (Apr 18, 2023)2538519
12-122328099-T-A not specified Uncertain significance (Nov 19, 2015)434778

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
CLIP1protein_codingprotein_codingENST00000540338 25151201
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.6810.31912560601421257480.000565
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense2.085897490.7870.00004099488
Missense in Polyphen313442.010.708135691
Synonymous-0.9443142931.070.00001762650
Loss of Function6.071569.70.2150.00000356920

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0008470.000846
Ashkenazi Jewish0.002530.00199
East Asian0.0003300.000326
Finnish0.0001430.000139
European (Non-Finnish)0.0005720.000545
Middle Eastern0.0003300.000326
South Asian0.0009440.000752
Other0.001260.00114

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

AllRecessiveDominant
MendelianHighHighHigh
Primary ImmunodeficiencyHighHighHigh
CancerHighHighHigh

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