LYL1

LYL1 basic helix-loop-helix family member, the group of Basic helix-loop-helix proteins

Basic information

Region (hg38): 19:13099033-13103161

Links

ENSG00000104903 ∙ NCBI:4066 ∙ OMIM:151440 ∙ HGNC:6734 ∙ Uniprot:P12980 ∙ 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 LYL1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LYL1 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			23			23
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	23	0	0

Variants in LYL1

This is a list of pathogenic ClinVar variants found in the LYL1 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-13099323-C-T		not specified	Uncertain significance (Dec 07, 2021)
19-13099353-A-C		not specified	Uncertain significance (Mar 02, 2023)
19-13099394-G-T		not specified	Uncertain significance (Jun 29, 2023)
19-13099405-G-A		not specified	Uncertain significance (Mar 01, 2023)
19-13099479-T-C		not specified	Uncertain significance (Jan 09, 2024)
19-13099506-G-A		not specified	Uncertain significance (Mar 30, 2024)
19-13099506-G-T		not specified	Uncertain significance (Dec 27, 2023)
19-13099564-C-T		not specified	Uncertain significance (Nov 07, 2022)
19-13099602-C-G		not specified	Uncertain significance (Aug 02, 2023)
19-13099638-T-C		not specified	Uncertain significance (Jul 19, 2023)
19-13099652-G-T		not specified	Uncertain significance (May 02, 2023)
19-13099674-T-A		not specified	Uncertain significance (Mar 28, 2024)
19-13099689-C-T		not specified	Uncertain significance (Nov 01, 2022)
19-13100683-C-T		not specified	Uncertain significance (Mar 19, 2024)
19-13100701-C-T		not specified	Uncertain significance (Nov 08, 2022)
19-13100728-C-A		not specified	Uncertain significance (Dec 16, 2023)
19-13100743-T-C		not specified	Uncertain significance (Jul 27, 2021)
19-13100871-C-T		not specified	Uncertain significance (Oct 26, 2022)
19-13100882-G-A		not specified	Uncertain significance (Feb 27, 2023)
19-13100922-G-A		not specified	Uncertain significance (Dec 05, 2022)
19-13100939-G-T		not specified	Uncertain significance (Jan 05, 2022)
19-13100948-A-T		not specified	Uncertain significance (May 23, 2023)
19-13100958-C-T		not specified	Uncertain significance (Sep 06, 2022)
19-13101040-C-G		not specified	Uncertain significance (May 24, 2023)
19-13101099-T-G		not specified	Uncertain significance (Oct 06, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LYL1	protein_coding	protein_coding	ENST00000264824	3	4129

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.773	0.220	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.950	85	113	0.749	0.00000690	1715
Missense in Polyphen		26	44.481	0.58452		591
Synonymous	-0.0772	50	49.3	1.01	0.00000280	646
Loss of Function	2.05	0	4.90	0.00	2.42e-7	66

LoF frequencies by population

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

dbNSFP

Source: dbNSFP

• Disease: DISEASE: Note=A chromosomal aberration involving LYL1 may be a cause of a form of T-cell acute lymphoblastic leukemia (T-ALL). Translocation t(7;19)(q35;p13) with TCRB.
• Pathway: Transcriptional misregulation in cancer - Homo sapiens (human);Hematopoietic Stem Cell Differentiation;Imatinib and Chronic Myeloid Leukemia;TYROBP Causal Network (Consensus)

Recessive Scores

• pRec: 0.180

Haploinsufficiency Scores

• pHI: 0.131
• hipred: N
• hipred_score: 0.392

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: K
• gene_indispensability_pred: E
• gene_indispensability_score: 0.990

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lyl1
• Phenotype: immune system phenotype; hematopoietic system phenotype

Gene ontology

• Biological process: blood vessel maturation;regulation of transcription, DNA-templated;regulation of transcription by RNA polymerase II;B cell differentiation;positive regulation of transcription, DNA-templated;definitive hemopoiesis
• Cellular component: nucleus
• Molecular function: RNA polymerase II regulatory region sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA binding;protein binding;protein dimerization activity