HLF

HLF transcription factor, PAR bZIP family member, the group of PAR bZIP family

Basic information

Region (hg38): 17:55264959-55325187

Links

ENSG00000108924 ∙ NCBI:3131 ∙ OMIM:142385 ∙ HGNC:4977 ∙ Uniprot:Q16534 ∙ 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 HLF gene.

• Inborn genetic diseases (11 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HLF 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			11			11
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	11	0	1

Variants in HLF

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

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

Position	Type	Phenotype	Significance	ClinVar
17-55265540-A-G		not specified	Uncertain significance (Oct 22, 2021)
17-55265559-G-A			Benign (Jul 13, 2018)
17-55265570-C-T		not specified	Uncertain significance (Jun 11, 2021)
17-55265587-C-T		not specified	Uncertain significance (Aug 28, 2023)
17-55267768-G-A		not specified	Uncertain significance (Jan 22, 2024)
17-55267893-G-T		not specified	Uncertain significance (Oct 13, 2023)
17-55267970-G-T		not specified	Uncertain significance (Feb 27, 2024)
17-55268020-C-T		not specified	Uncertain significance (Nov 22, 2021)
17-55268070-G-GA		Malignant tumor of prostate	Uncertain significance (-)
17-55268083-C-G		not specified	Uncertain significance (Dec 05, 2022)
17-55315247-C-T		not specified	Uncertain significance (Jan 23, 2023)
17-55315303-G-C		not specified	Uncertain significance (Dec 15, 2022)
17-55315368-G-A		not specified	Uncertain significance (Sep 28, 2021)
17-55315406-A-T		not specified	Uncertain significance (Jun 11, 2021)
17-55315408-C-G		not specified	Uncertain significance (Mar 14, 2023)
17-55320719-G-A		not specified	Uncertain significance (Jul 14, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HLF	protein_coding	protein_coding	ENST00000226067	4	60054

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.952	0.0477	125690	0	2	125692	0.00000796

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.28	94	180	0.521	0.0000105	1941
Missense in Polyphen		29	86.787	0.33415		915
Synonymous	0.208	71	73.3	0.969	0.00000430	587
Loss of Function	2.86	0	9.55	0.00	4.08e-7	122

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)	0.00000880	0.00000880
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

• Disease: DISEASE: Note=A chromosomal aberration involving HLF is a cause of pre-B-cell acute lymphoblastic leukemia (B-ALL). Translocation t(17;19)(q22;p13.3) with TCF3.

Recessive Scores

• pRec: 0.136

Intolerance Scores

• rvis_EVS: -0.32
• rvis_percentile_EVS: 31.46

Haploinsufficiency Scores

• pHI: 0.471
• hipred: Y
• hipred_score: 0.728
• ghis: 0.619

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.849

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Hlf
• Phenotype: liver/biliary system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); normal phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); homeostasis/metabolism phenotype

Gene ontology

• Biological process: transcription by RNA polymerase II;multicellular organism development;skeletal muscle cell differentiation;positive regulation of transcription by RNA polymerase II;rhythmic process
• 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 transcription activator activity, RNA polymerase II-specific;DNA binding;double-stranded DNA binding;sequence-specific DNA binding