CLVS2

clavesin 2

Basic information

Region (hg38): 6:122996235-123072925

Previous symbols: [ "C6orf212", "C6orf213", "RLBP1L2" ]

Links

ENSG00000146352 ∙ NCBI:134829 ∙ OMIM:616945 ∙ HGNC:23046 ∙ Uniprot:Q5SYC1 ∙ 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 CLVS2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CLVS2 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				1		1
missense			15			15
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	15	1	0

Variants in CLVS2

This is a list of pathogenic ClinVar variants found in the CLVS2 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-122997803-C-G		not specified	Uncertain significance (Apr 20, 2023)
6-122997830-T-A		not specified	Uncertain significance (Aug 05, 2024)
6-122997832-G-C		not specified	Uncertain significance (Jan 26, 2025)
6-122997919-C-T		not specified	Uncertain significance (Dec 15, 2022)
6-122997949-T-G		not specified	Uncertain significance (Jan 21, 2025)
6-122998030-A-C		not specified	Uncertain significance (Jul 06, 2021)
6-123011011-C-G		not specified	Uncertain significance (Dec 20, 2023)
6-123011102-C-G		not specified	Uncertain significance (Aug 12, 2021)
6-123011133-C-A		not specified	Uncertain significance (Feb 13, 2024)
6-123048636-G-A			Likely benign (Mar 01, 2023)
6-123048691-A-T		not specified	Uncertain significance (Oct 04, 2023)
6-123048700-C-T		not specified	Uncertain significance (Oct 25, 2022)
6-123055851-C-A		not specified	Uncertain significance (Dec 21, 2022)
6-123055920-A-T		not specified	Uncertain significance (Nov 10, 2024)
6-123055978-T-C		not specified	Uncertain significance (Nov 15, 2021)
6-123055992-G-A		not specified	Uncertain significance (Feb 15, 2023)
6-123063718-A-G		not specified	Uncertain significance (Sep 30, 2024)
6-123063724-A-G		not specified	Uncertain significance (Nov 25, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CLVS2	protein_coding	protein_coding	ENST00000275162	5	76957

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0136	0.958	125742	0	6	125748	0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.80	116	185	0.627	0.0000106	2170
Missense in Polyphen		16	59.403	0.26935		704
Synonymous	-0.0222	72	71.8	1.00	0.00000403	630
Loss of Function	1.91	5	12.2	0.409	6.02e-7	148

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000545	0.0000544
Finnish	0.0000476	0.0000462
European (Non-Finnish)	0.0000276	0.0000264
Middle Eastern	0.0000545	0.0000544
South Asian	0.0000327	0.0000327
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: Lysosome Vesicle Biogenesis;Clathrin derived vesicle budding;trans-Golgi Network Vesicle Budding;Vesicle-mediated transport;Membrane Trafficking (Consensus)

Intolerance Scores

• loftool: 0.310
• rvis_EVS: -0.01
• rvis_percentile_EVS: 53.19

Haploinsufficiency Scores

• pHI: 0.201
• hipred: Y
• hipred_score: 0.736
• ghis: 0.594

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Clvs2

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