NFYB
Basic information
Region (hg38): 12:104117086-104138241
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (8 variants)
- not_provided (1 variants)
- EBV-positive_nodal_T-_and_NK-cell_lymphoma (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the NFYB gene is commonly pathogenic or not. These statistics are base on transcript: NM_000006166.4. 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 | 2 | |||||
| missense | 8 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 8 | 2 | 0 |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| NFYB | protein_coding | protein_coding | ENST00000240055 | 7 | 21213 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.000250 | 0.783 | 125718 | 0 | 20 | 125738 | 0.0000795 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.18 | 45 | 109 | 0.412 | 0.00000509 | 1382 |
| Missense in Polyphen | 7 | 31.582 | 0.22165 | 417 | ||
| Synonymous | -0.143 | 34 | 33.0 | 1.03 | 0.00000161 | 360 |
| Loss of Function | 1.09 | 7 | 10.9 | 0.643 | 4.56e-7 | 150 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000187 | 0.000185 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.000141 | 0.000139 |
| European (Non-Finnish) | 0.000126 | 0.000123 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Component of the sequence-specific heterotrimeric transcription factor (NF-Y) which specifically recognizes a 5'- CCAAT-3' box motif found in the promoters of its target genes. NF- Y can function as both an activator and a repressor, depending on its interacting cofactors.;
- Pathway
- Antigen processing and presentation - Homo sapiens (human);HTLV-I infection - Homo sapiens (human);Tuberculosis - Homo sapiens (human);overview of telomerase rna component gene hterc transcriptional regulation;Metabolism of lipids;Regulation of cholesterol biosynthesis by SREBP (SREBF);Metabolism;Metabolism of steroids;TGF_beta_Receptor;Direct p53 effectors;Activation of gene expression by SREBF (SREBP);Validated targets of C-MYC transcriptional repression
(Consensus)
Recessive Scores
- pRec
- 0.240
Intolerance Scores
- loftool
- 0.563
- rvis_EVS
- 0.1
- rvis_percentile_EVS
- 60.96
Haploinsufficiency Scores
- pHI
- 0.826
- hipred
- Y
- hipred_score
- 0.673
- ghis
- 0.683
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 1.00
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Nfyb
- Phenotype
Zebrafish Information Network
- Gene name
- nfybb
- Affected structure
- ceratobranchial cartilage
- Phenotype tag
- abnormal
- Phenotype quality
- aplastic
Gene ontology
- Biological process
- regulation of transcription, DNA-templated;regulation of transcription by RNA polymerase II;regulation of cholesterol biosynthetic process;positive regulation of transcription, DNA-templated;cellular response to leukemia inhibitory factor
- Cellular component
- nucleus;nucleoplasm;CCAAT-binding factor complex;protein-DNA complex;RNA polymerase II transcription factor complex
- Molecular function
- RNA polymerase II distal enhancer sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA binding;DNA-binding transcription factor activity;protein binding;transcription regulatory region DNA binding;protein-containing complex binding;protein heterodimerization activity;repressing transcription factor binding