LYL1

protein-coding

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

Gene summary

This gene represents a basic helix-loop-helix transcription factor. The encoded protein may play roles in blood vessel maturation and hematopoeisis. A translocation between this locus and the T cell receptor beta locus (GeneID 6957) on chromosome 7 has been associated with acute lymphoblastic leukemia. [provided by RefSeq, Sep 2010]

MANE transcript

NM_005583.5

Inheritance

—

ClinVar variants

U:59B:2

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0

Max pathogenic AF

—

Genomic locus

chr19:13,099,033-13,103,161

External References & Databases

Ensembl (ENSG00000104903)

Transcript & Mutation Effects

hg38 • Region Span ~4.1 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to LYL1 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 60

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_005583.5. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			58 clinvar	2 clinvar		60
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	59	2	0	61

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 10 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_005583.5	RefSeq	NP_005574.2	3	MANE Select
ENST00000264824.5	Ensembl	ENSP00000264824.3	3	MANE Select
ENST00000590974.1	Ensembl	ENSP00000468122.1	2	Standard
ENST00000892171.1	Ensembl	ENSP00000562230.1	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Transcriptional misregulation in cancer - Homo sapiens (human)
Hematopoietic Stem Cell Differentiation
Imatinib and Chronic Myeloid Leukemia
TYROBP Causal Network

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

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

Cellular Component

nucleus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000264824
Coding exons: 3
Length: 4129
Individuals with no LoFs: 0
Homozygous LoFs: 0
Heterozygous LoFs: 0
Defined: 0
p: 0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.950	85	113	0.749	0.00000690	1715
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0	0.0	absent
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

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.;

Recessive Scores

pRec: 0.180

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): K
Indispensability pred.: E
Indispensability score: 0.990

Gene Damage Prediction

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