COBLL1

cordon-bleu WH2 repeat protein like 1, the group of Small nucleolar RNA protein coding host genes

Basic information

Region (hg38): 2:164653623-164843679

Links

ENSG00000082438 ∙ NCBI:22837 ∙ OMIM:610318 ∙ HGNC:23571 ∙ Uniprot:Q53SF7 ∙ 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 COBLL1 gene.

• Inborn genetic diseases (47 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the COBLL1 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			43	4		47
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	43	5	0

Variants in COBLL1

This is a list of pathogenic ClinVar variants found in the COBLL1 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-164692316-T-C		not specified	Uncertain significance (May 23, 2023)
2-164694315-G-T		not specified	Uncertain significance (Dec 06, 2021)
2-164694378-T-G		not specified	Uncertain significance (Mar 07, 2024)
2-164694385-G-A		not specified	Uncertain significance (Mar 04, 2024)
2-164694394-T-G		not specified	Uncertain significance (May 25, 2022)
2-164694432-G-A		not specified	Uncertain significance (Jun 08, 2022)
2-164694543-G-T		not specified	Uncertain significance (Jun 02, 2023)
2-164694574-C-T		not specified	Likely benign (Jul 27, 2021)
2-164694673-C-T		not specified	Uncertain significance (Dec 26, 2023)
2-164694682-C-T		not specified	Uncertain significance (Jun 18, 2021)
2-164694721-C-T		not specified	Uncertain significance (Jun 09, 2022)
2-164694765-G-A		not specified	Uncertain significance (May 03, 2023)
2-164694771-C-G		not specified	Uncertain significance (Jun 27, 2022)
2-164694817-T-C		not specified	Uncertain significance (Sep 25, 2023)
2-164694946-C-T		not specified	Uncertain significance (Aug 16, 2022)
2-164694966-G-A		not specified	Uncertain significance (May 31, 2022)
2-164694992-A-C			Likely benign (Aug 01, 2023)
2-164695076-A-T		not specified	Uncertain significance (Jun 26, 2023)
2-164695087-T-G		not specified	Uncertain significance (Mar 23, 2023)
2-164695189-T-C		not specified	Uncertain significance (Dec 28, 2022)
2-164695194-G-A		not specified	Uncertain significance (Mar 01, 2024)
2-164695195-T-C		not specified	Uncertain significance (Oct 13, 2023)
2-164695354-G-T		not specified	Uncertain significance (Mar 05, 2024)
2-164695372-T-C		not specified	Uncertain significance (Jun 05, 2023)
2-164695383-G-A		not specified	Uncertain significance (Dec 07, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
COBLL1	protein_coding	protein_coding	ENST00000342193	14	190056

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0467	0.953	125695	0	53	125748	0.000211

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.216	616	601	1.02	0.0000290	7677
Missense in Polyphen		181	186.32	0.97147		2413
Synonymous	-0.585	231	220	1.05	0.0000116	2260
Loss of Function	4.43	11	42.0	0.262	0.00000213	579

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000119	0.000119
Ashkenazi Jewish	0.00	0.00
East Asian	0.000767	0.000761
Finnish	0.0000926	0.0000924
European (Non-Finnish)	0.000116	0.000114
Middle Eastern	0.000767	0.000761
South Asian	0.000688	0.000686
Other	0.000167	0.000163

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0860

Intolerance Scores

• loftool: 0.0845
• rvis_EVS: 0.41
• rvis_percentile_EVS: 76.54

Haploinsufficiency Scores

• pHI: 0.610
• hipred: N
• hipred_score: 0.233
• ghis: 0.457

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.513

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cobll1

Zebrafish Information Network

• Gene name: cobll1b
• Affected structure: myeloid cell
• Phenotype tag: abnormal
• Phenotype quality: decreased amount

Gene ontology

• Cellular component: extracellular exosome
• Molecular function: actin monomer binding;cadherin binding