CLVS1

clavesin 1

Basic information

Region (hg38): 8:61057157-61501645

Previous symbols: [ "RLBP1L1" ]

Links

ENSG00000177182 ∙ NCBI:157807 ∙ OMIM:611292 ∙ HGNC:23139 ∙ Uniprot:Q8IUQ0 ∙ 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 CLVS1 gene.

• Inborn genetic diseases (5 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CLVS1 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			5			5
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	5	0	0

Variants in CLVS1

This is a list of pathogenic ClinVar variants found in the CLVS1 region.

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

Position	Type	Phenotype	Significance	ClinVar
8-61299931-T-C		not specified	Uncertain significance (Dec 26, 2023)
8-61299952-T-C		not specified	Uncertain significance (Oct 13, 2023)
8-61299989-G-T		not specified	Uncertain significance (Nov 15, 2021)
8-61300143-G-A		not specified	Uncertain significance (Dec 19, 2023)
8-61376667-C-T		not specified	Uncertain significance (Nov 27, 2023)
8-61454181-A-G		not specified	Uncertain significance (Sep 01, 2021)
8-61454213-C-T		not specified	Uncertain significance (Apr 27, 2023)
8-61458343-C-G		not specified	Uncertain significance (Aug 08, 2023)
8-61458422-C-T		not specified	Uncertain significance (Jan 04, 2022)
8-61458436-G-A		not specified	Uncertain significance (Sep 29, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CLVS1	protein_coding	protein_coding	ENST00000519846	5	444488

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.854	0.146	125725	0	8	125733	0.0000318

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.41	146	203	0.720	0.0000112	2335
Missense in Polyphen		27	64.114	0.42112		767
Synonymous	0.0111	81	81.1	0.998	0.00000487	683
Loss of Function	3.12	2	15.1	0.133	8.09e-7	175

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000185	0.000185
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000463	0.0000462
European (Non-Finnish)	0.0000353	0.0000352
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Required for normal morphology of late endosomes and/or lysosomes in neurons (By similarity). Binds phosphatidylinositol 3,5-bisphosphate (PtdIns(3,5)P2). {ECO:0000250, ECO:0000269|PubMed:19651769}.
• Pathway: Ectoderm Differentiation;Lysosome Vesicle Biogenesis;Clathrin derived vesicle budding;trans-Golgi Network Vesicle Budding;Vesicle-mediated transport;Membrane Trafficking (Consensus)

Intolerance Scores

• loftool: 0.0763
• rvis_EVS: -0.49
• rvis_percentile_EVS: 22.09

Haploinsufficiency Scores

• pHI: 0.649
• hipred: Y
• hipred_score: 0.654
• ghis: 0.637

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.231

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Clvs1
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); 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); skeleton phenotype; growth/size/body region phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: lysosome organization
• Cellular component: endosome;trans-Golgi network;clathrin-coated vesicle;early endosome membrane;trans-Golgi network membrane
• Molecular function: phosphatidylinositol-3,5-bisphosphate binding