NFYC
nuclear transcription factor Y subunit gamma, the group of MicroRNA protein coding host genes
Basic information
Region (hg38): 1:40691648-40771603
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the NFYC 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 | 0 | |||||
| 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 | 0 |
Variants in NFYC
This is a list of pathogenic ClinVar variants found in the NFYC region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 1-40758127-G-A | not specified | Uncertain significance (Aug 26, 2024) | ||
| 1-40758193-G-A | not specified | Uncertain significance (Jan 17, 2025) | ||
| 1-40762903-A-G | not specified | Uncertain significance (Oct 12, 2024) | ||
| 1-40762932-G-C | not specified | Uncertain significance (May 20, 2024) | ||
| 1-40762951-C-G | not specified | Uncertain significance (Jun 17, 2024) | ||
| 1-40762969-G-T | not specified | Uncertain significance (Sep 16, 2021) | ||
| 1-40766608-G-A | not specified | Uncertain significance (Jul 27, 2024) | ||
| 1-40766641-C-G | not specified | Uncertain significance (Mar 23, 2022) | ||
| 1-40766940-G-A | not specified | Uncertain significance (Feb 22, 2023) | ||
| 1-40770736-A-G | not specified | Uncertain significance (Sep 15, 2021) | ||
| 1-40770737-T-C | not specified | Uncertain significance (Dec 11, 2024) | ||
| 1-40770757-G-A | not specified | Uncertain significance (Oct 09, 2024) | ||
| 1-40770798-C-A | not specified | Uncertain significance (Feb 14, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| NFYC | protein_coding | protein_coding | ENST00000425457 | 10 | 79956 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.108 | 0.891 | 125738 | 0 | 10 | 125748 | 0.0000398 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.52 | 104 | 206 | 0.506 | 0.0000116 | 2326 |
| Missense in Polyphen | 51 | 106.5 | 0.47889 | 1266 | ||
| Synonymous | 0.833 | 67 | 76.2 | 0.879 | 0.00000449 | 671 |
| Loss of Function | 3.54 | 7 | 26.8 | 0.261 | 0.00000137 | 246 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000152 | 0.000152 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.000140 | 0.000139 |
| European (Non-Finnish) | 0.0000353 | 0.0000352 |
| 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);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
- 0.119
Intolerance Scores
- loftool
- 0.605
- rvis_EVS
- -0.43
- rvis_percentile_EVS
- 25.15
Haploinsufficiency Scores
- pHI
- 0.696
- hipred
- Y
- hipred_score
- 0.699
- ghis
- 0.652
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.716
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Nfyc
- Phenotype
Zebrafish Information Network
- Gene name
- nfyc
- Affected structure
- head
- Phenotype tag
- abnormal
- Phenotype quality
- decreased size
Gene ontology
- Biological process
- regulation of transcription, DNA-templated;regulation of transcription by RNA polymerase II;protein folding;regulation of cholesterol biosynthetic process;positive regulation of transcription by RNA polymerase II
- 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;transcription coactivator activity;protein binding;transcription factor binding;transcription regulatory region DNA binding;protein heterodimerization activity