CLINT1

clathrin interactor 1

Basic information

Region (hg38): 5:157785742-157859145

Links

ENSG00000113282 ∙ NCBI:9685 ∙ OMIM:607265 ∙ HGNC:23186 ∙ Uniprot:Q14677 ∙ 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 CLINT1 gene.

• Inborn genetic diseases (20 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CLINT1 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			18	2		20
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	18	2	0

Variants in CLINT1

This is a list of pathogenic ClinVar variants found in the CLINT1 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-157787747-T-C		not specified	Uncertain significance (Oct 26, 2021)
5-157787765-C-T		not specified	Likely benign (Jun 11, 2021)
5-157787818-G-C		not specified	Uncertain significance (Feb 11, 2022)
5-157787828-G-A		not specified	Uncertain significance (Nov 07, 2023)
5-157787855-T-G		not specified	Uncertain significance (Feb 17, 2023)
5-157787860-T-C		not specified	Likely benign (Nov 17, 2022)
5-157787899-T-C		not specified	Uncertain significance (Feb 10, 2023)
5-157787930-A-T		not specified	Uncertain significance (Mar 05, 2024)
5-157789376-C-G		not specified	Uncertain significance (Sep 14, 2022)
5-157789417-T-C		not specified	Uncertain significance (May 22, 2023)
5-157789423-G-A		not specified	Uncertain significance (Aug 02, 2022)
5-157789503-A-G		not specified	Uncertain significance (Sep 21, 2021)
5-157789521-T-C		not specified	Uncertain significance (Dec 28, 2023)
5-157789525-G-C		not specified	Uncertain significance (Oct 26, 2022)
5-157791840-G-C		not specified	Uncertain significance (May 11, 2022)
5-157791846-G-C		not specified	Uncertain significance (Jan 09, 2024)
5-157791884-G-A		not specified	Uncertain significance (Apr 13, 2023)
5-157791941-G-T		not specified	Uncertain significance (Dec 08, 2023)
5-157791980-C-T		not specified	Uncertain significance (Jan 31, 2024)
5-157791986-G-T		not specified	Uncertain significance (Feb 13, 2024)
5-157803687-G-T		not specified	Uncertain significance (Dec 07, 2023)
5-157805888-T-G		not specified	Uncertain significance (Mar 24, 2023)
5-157805891-G-A		not specified	Uncertain significance (Aug 12, 2022)
5-157806059-A-T		not specified	Uncertain significance (Sep 29, 2022)
5-157806071-G-A		not specified	Uncertain significance (Feb 10, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CLINT1	protein_coding	protein_coding	ENST00000523908	12	73433

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.535	0.465	124596	0	10	124606	0.0000401

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.54	270	351	0.768	0.0000175	4263
Missense in Polyphen		62	118.58	0.52284		1456
Synonymous	1.13	103	119	0.868	0.00000622	1190
Loss of Function	4.17	7	32.8	0.213	0.00000178	377

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000176	0.000176
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000557	0.0000556
Finnish	0.00	0.00
European (Non-Finnish)	0.0000185	0.0000177
Middle Eastern	0.0000557	0.0000556
South Asian	0.0000361	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Binds to membranes enriched in phosphatidylinositol 4,5- bisphosphate (PtdIns(4,5)P2). May have a role in transport via clathrin-coated vesicles from the trans-Golgi network to endosomes. Stimulates clathrin assembly. {ECO:0000269|PubMed:12429846, ECO:0000269|PubMed:12538641}.
• Pathway: Golgi Associated Vesicle Biogenesis;Clathrin derived vesicle budding;trans-Golgi Network Vesicle Budding;Vesicle-mediated transport;Membrane Trafficking;Fibroblast growth factor-1 (Consensus)

Recessive Scores

• pRec: 0.137

Intolerance Scores

• loftool: 0.721
• rvis_EVS: -0.29
• rvis_percentile_EVS: 33.2

Haploinsufficiency Scores

• pHI: 0.668
• hipred: Y
• hipred_score: 0.792
• ghis: 0.580

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.850

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Clint1

Zebrafish Information Network

• Gene name: clint1a
• Affected structure: trunk
• Phenotype tag: abnormal
• Phenotype quality: decreased size

Gene ontology

• Biological process: endocytosis;clathrin coat assembly
• Cellular component: nucleoplasm;Golgi apparatus;cytosol;membrane;clathrin-coated vesicle;intracellular membrane-bounded organelle;perinuclear region of cytoplasm
• Molecular function: protein binding;lipid binding;clathrin binding;cadherin binding