CLIP1

CAP-Gly domain containing linker protein 1

Basic information

Region (hg38): 12:122271431-122422669

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.

• 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	16	5	24
missense			53	3		56
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)			1			1
splice region			1		1	2
non coding			1	1	1	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		not specified	Uncertain significance (Aug 12, 2021)
12-122272933-T-A		not specified	Uncertain significance (Jan 16, 2024)
12-122272966-T-C		not specified	Uncertain significance (Dec 30, 2016)
12-122273011-G-C		not specified	Uncertain significance (Aug 01, 2022)
12-122273074-T-C		Global developmental delay	Uncertain significance (Jan 16, 2020)
12-122274063-C-T		not specified	Uncertain significance (Nov 15, 2021)
12-122274122-T-C		not specified	Uncertain significance (Jun 22, 2023)
12-122274131-A-G		not specified	Uncertain significance (Oct 05, 2023)
12-122274172-T-TA		not specified	Benign (Sep 23, 2019)
12-122278178-C-G		not specified	Uncertain significance (Dec 08, 2023)
12-122278196-T-C			Benign (Dec 05, 2017)
12-122278783-G-A			Likely benign (May 25, 2018)
12-122278800-C-G		not specified	Uncertain significance (Sep 16, 2021)
12-122278859-G-C			Likely benign (Dec 31, 2019)
12-122278880-T-C		not specified	Likely benign (Jul 21, 2016)
12-122278908-T-C		CLIP1-related intellectual disability • not specified	Uncertain significance (Apr 12, 2022)
12-122278919-G-A		CLIP1-related disorder	Likely benign (Sep 11, 2019)
12-122279084-T-A		not specified	Uncertain significance (Mar 06, 2018)
12-122279123-C-A			Likely benign (Dec 31, 2019)
12-122309789-G-A			Likely benign (Oct 01, 2022)
12-122309834-C-T		CLIP1-related disorder	Likely benign (Aug 09, 2019)
12-122316781-C-A		not specified	Uncertain significance (Jan 19, 2024)
12-122316786-C-T		not specified	Uncertain significance (Dec 12, 2023)
12-122316808-G-C		not specified	Uncertain significance (Feb 28, 2020)
12-122319262-G-A		not specified	Likely benign (Jun 21, 2018)

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