ID4

inhibitor of DNA binding 4, the group of Basic helix-loop-helix proteins

Basic information

Region (hg38): 6:19837370-19842197

Links

ENSG00000172201

∙ NCBI:3400 ∙ OMIM:600581 ∙ HGNC:5363 ∙ Uniprot:P47928 ∙ 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 ID4 gene.

not_specified (25 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ID4 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000001546.4. 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						0
missense			25 clinvar			25
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	25	0	0

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ID4	protein_coding	protein_coding	ENST00000378700	2	3299

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0312	0.618	125517	0	8	125525	0.0000319

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.855	77	58.6	1.31	0.00000261	989
Missense in Polyphen		18	19.207	0.93715		289
Synonymous	-4.16	56	28.0	2.00	0.00000131	355
Loss of Function	0.233	2	2.39	0.837	1.01e-7	44

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)	0.0000371	0.0000353
Middle Eastern	0.00	0.00
South Asian	0.0000653	0.0000653
Other	0.000327	0.000327

dbNSFP

Source: dbNSFP

Function: FUNCTION: Transcriptional regulator (lacking a basic DNA binding domain) which negatively regulates the basic helix-loop-helix (bHLH) transcription factors by forming heterodimers and inhibiting their DNA binding and transcriptional activity. Implicated in regulating a variety of cellular processes, including cellular growth, senescence, differentiation, apoptosis, angiogenesis, and neoplastic transformation (By similarity). {ECO:0000250}.;
Pathway: TGF-beta signaling pathway - Homo sapiens (human);Signaling pathways regulating pluripotency of stem cells - Homo sapiens (human);Vitamin D Receptor Pathway;ID (Consensus)

Recessive Scores

pRec: 0.194

Haploinsufficiency Scores

pHI: 0.277
hipred: Y
hipred_score: 0.546
ghis: 0.620

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.647

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Id4
Phenotype: reproductive system 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); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); skeleton 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); endocrine/exocrine gland phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); growth/size/body region phenotype; cellular phenotype; homeostasis/metabolism phenotype;

Gene ontology

Biological process: G1/S transition of mitotic cell cycle;negative regulation of transcription by RNA polymerase II;regulation of transcription by RNA polymerase II;neuroblast proliferation;circadian rhythm;positive regulation of cell population proliferation;hippocampus development;cerebral cortex neuron differentiation;central nervous system myelination;neuron differentiation;cellular protein localization;negative regulation of DNA binding;fat cell differentiation;negative regulation of fat cell differentiation;negative regulation of neuron differentiation;positive regulation of osteoblast differentiation;negative regulation of transcription, DNA-templated;positive regulation of transcription by RNA polymerase II;negative regulation of astrocyte differentiation;negative regulation of oligodendrocyte differentiation;regulation of cell cycle;prostate gland epithelium morphogenesis;prostate gland stromal morphogenesis;seminal vesicle morphogenesis
Cellular component: nucleus;cytoplasm
Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;RNA polymerase II transcription factor binding;DNA-binding transcription factor activity;transcription corepressor activity;protein binding;transcription factor binding;protein dimerization activity