NFYB

protein-coding

nuclear transcription factor Y subunit beta

Gene summary

The protein encoded by this gene is one subunit of a trimeric complex, forming a highly conserved transcription factor that binds with high specificity to CCAAT motifs in the promoter regions in a variety of genes. This gene product, subunit B, forms a tight dimer with the C subunit, a prerequisite for subunit A association. The resulting trimer binds to DNA with high specificity and affinity. Subunits B and C each contain a histone-like motif. Observation of the histone nature of these subunits is supported by two types of evidence; protein sequence alignments and experiments with mutants. [provided by RefSeq, Jul 2008]

MANE transcript

NM_006166.4

Inheritance

—

ClinVar variants

U:15B:2

Top phenotype

EBV-positive nodal T- and NK-cell lymphoma

gnomAD constraint

pLI —, LoF o/e 0.64

Max pathogenic AF

—

Genomic locus

chr12:104,117,086-104,138,241

External References & Databases

Ensembl (ENSG00000120837)

Transcript & Mutation Effects

hg38 • Region Span ~21.2 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to NFYB variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 11

EBV-positive nodal T- and NK-cell lymphomaTotal: 1

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_006166.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous				2 clinvar		2
missense			12 clinvar			12
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	15	2	0	17

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 57 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_006166.4	RefSeq	NP_006157.1	7	MANE Select
ENST00000240055.8	Ensembl	ENSP00000240055.3	7	MANE Select
NM_001414518.1	RefSeq	NP_001401447.1	7	Standard
NM_001414519.1	RefSeq	NP_001401448.1	7	Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / Model	Organism	Observed Phenotype
nfybb	Danio rerio	Structure: ceratobranchial cartilage Quality: aplastic abnormal

Gene / Model

Organism

Observed Phenotype

nfybb

Danio rerio

Structure: ceratobranchial cartilage

Quality: aplastic

abnormal

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

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

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

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

Cellular Component

nucleus
nucleoplasm
CCAAT-binding factor complex
protein-DNA complex
RNA polymerase II transcription factor complex

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000240055
Coding exons: 7
Length: 21213
Individuals with no LoFs: 125718
Homozygous LoFs: 0
Heterozygous LoFs: 20
Defined: 125738
p: 0.0000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.18	45	109	0.412	0.00000509	1382
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00019	0.00018	rare
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0.00014	0.00014	rare
European (Non-Finnish)	0.00013	0.00012	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

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.;

Recessive Scores

pRec: 0.240

Intolerance Scores

LoFtool: 0.563
RVIS EVS: 0.1
RVIS percentile EVS: 60.96

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): E
Indispensability pred.: E
Indispensability score: 1.00

Gene Damage Prediction

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