CLLU1

chronic lymphocytic leukemia up-regulated 1, the group of Long non-coding RNAs with non-systematic symbols

Basic information

Region (hg38): 12:92421531-92431002

Links

ENSG00000257127 ∙ NCBI:574028 ∙ OMIM:616988 ∙ HGNC:29841 ∙ Uniprot:Q5K131 ∙ 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 CLLU1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CLLU1 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						0
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			3			3
Total	0	0	3	0	0

Variants in CLLU1

This is a list of pathogenic ClinVar variants found in the CLLU1 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-92422565-G-C		not specified	Uncertain significance (Sep 25, 2024)
12-92422570-G-C		not specified	Uncertain significance (Dec 06, 2022)
12-92422628-G-C		not specified	Uncertain significance (Jul 06, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CLLU1	protein_coding	protein_coding	ENST00000378485	1	9472

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00167	0.480	122517	14	2194	124725	0.00889

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.815	78	60.2	1.30	0.00000297	801
Missense in Polyphen		2	1.5058	1.3282		18
Synonymous	-0.521	26	22.8	1.14	0.00000124	215
Loss of Function	0.0268	4	4.06	0.986	2.67e-7	55

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0400	0.0400
Ashkenazi Jewish	0.0190	0.0190
East Asian	0.000112	0.000111
Finnish	0.00684	0.00675
European (Non-Finnish)	0.00906	0.00902
Middle Eastern	0.000112	0.000111
South Asian	0.00237	0.00236
Other	0.0106	0.0105

dbNSFP

Source: dbNSFP

Haploinsufficiency Scores

• pHI: 0.101
• hipred: N
• hipred_score: 0.146
• ghis: 0.397

Essentials

• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0542

Gene Damage Prediction

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

Gene ontology

• Cellular component: cytoplasm