HELT

helt bHLH transcription factor, the group of Basic helix-loop-helix proteins

Basic information

Region (hg38): 4:185018490-185020953

Links

ENSG00000187821

∙ NCBI:391723 ∙ OMIM:617546 ∙ HGNC:33783 ∙ Uniprot:A6NFD8 ∙ 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 HELT gene.

not_specified (49 variants)
not_provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HELT gene is commonly pathogenic or not. These statistics are base on transcript: NM_001300781.2. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous				1 clinvar		1
missense			34 clinvar			34
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	34	1	0

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HELT	protein_coding	protein_coding	ENST00000338875	4	1964

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00101	0.831	125707	0	35	125742	0.000139

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.227	199	190	1.05	0.00000856	2080
Missense in Polyphen		57	63.496	0.89769		776
Synonymous	-1.57	105	86.4	1.22	0.00000399	700
Loss of Function	1.18	6	10.1	0.597	4.29e-7	120

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000279	0.000276
Ashkenazi Jewish	0.0000995	0.0000992
East Asian	0.000469	0.000435
Finnish	0.000325	0.000323
European (Non-Finnish)	0.000124	0.000123
Middle Eastern	0.000469	0.000435
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: Transcriptional repressor which binds preferentially to the canonical E box sequence 5'-CACGCG-3'. {ECO:0000250}.;

Recessive Scores

pRec: 0.191

Intolerance Scores

loftool: 0.355
rvis_EVS: -0.49
rvis_percentile_EVS: 22.36

Haploinsufficiency Scores

pHI: 0.392
hipred: N
hipred_score: 0.361
ghis: 0.444

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.862

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Helt
Phenotype: 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); growth/size/body region 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); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan);

Gene ontology

Biological process: negative regulation of transcription by RNA polymerase II;blood vessel development;suckling behavior;Notch signaling pathway;central nervous system development;heart development;post-embryonic development;multicellular organism aging;gene expression;GABAergic neuron differentiation in basal ganglia;cell differentiation;multicellular organism growth;positive regulation of transcription by RNA polymerase II;regulation of neurogenesis
Cellular component: nucleus;transcription factor complex
Molecular function: RNA polymerase II regulatory region sequence-specific DNA binding;RNA polymerase II proximal promoter sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;transcription corepressor activity;transcription factor binding;microsatellite binding;protein homodimerization activity;sequence-specific DNA binding;sequence-specific double-stranded DNA binding