NFYB

nuclear transcription factor Y subunit beta

Basic information

Region (hg38): 12:104117086-104138241

Links

ENSG00000120837 ∙ NCBI:4801 ∙ OMIM:189904 ∙ HGNC:7805 ∙ Uniprot:P25208 ∙ 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 NFYB gene.

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.

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			4			4
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	4	1	0

Variants in NFYB

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

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

Position	Type	Phenotype	Significance	ClinVar
12-104120411-A-G		not specified	Uncertain significance (Jul 25, 2023)
12-104123277-G-C			Likely benign (Aug 01, 2022)
12-104123334-T-C		EBV-positive nodal T- and NK-cell lymphoma	Likely benign (-)
12-104123387-C-T		not specified	Uncertain significance (Aug 16, 2021)
12-104128439-T-A		not specified	Uncertain significance (Dec 09, 2023)
12-104128460-T-C		not specified	Uncertain significance (Mar 25, 2022)

GnomAD

Source: gnomAD

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: dbNSFP

• 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

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