NFYA

nuclear transcription factor Y subunit alpha

Basic information

Region (hg38): 6:41072974-41102403

Links

ENSG00000001167

∙ NCBI:4800 ∙ OMIM:189903 ∙ HGNC:7804 ∙ Uniprot:P23511 ∙ 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 NFYA gene.

not_specified (15 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NFYA gene is commonly pathogenic or not. These statistics are base on transcript: NM_000002505.5. 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			15 clinvar			15
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	15	0	0

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NFYA	protein_coding	protein_coding	ENST00000341376	9	27032

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.146	0.854	125740	0	8	125748	0.0000318

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.78	85	194	0.438	0.00000991	2241
Missense in Polyphen		13	52.737	0.24651		522
Synonymous	-0.175	70	68.2	1.03	0.00000343	706
Loss of Function	3.32	6	23.3	0.258	0.00000119	218

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000616	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000264	0.0000264
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000655	0.0000653
Other	0.000164	0.000163

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. NF-YA positively regulates the transcription of the core clock component ARNTL/BMAL1. {ECO:0000269|PubMed:12741956}.;
Pathway: Antigen processing and presentation - Homo sapiens (human);Tuberculosis - Homo sapiens (human);Sterol Regulatory Element-Binding Proteins (SREBP) signalling;Wnt Signaling Pathway and Pluripotency;Sudden Infant Death Syndrome (SIDS) Susceptibility Pathways;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: 0.194

Intolerance Scores

loftool: 0.217
rvis_EVS: -0.21
rvis_percentile_EVS: 38.28

Haploinsufficiency Scores

pHI: 0.989
hipred: Y
hipred_score: 0.704
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: Nfya
Phenotype: cellular 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);

Gene ontology

Biological process: regulation of transcription, DNA-templated;regulation of transcription by RNA polymerase II;transcription by RNA polymerase II;regulation of cholesterol biosynthetic process;positive regulation of transcription, DNA-templated;rhythmic process
Cellular component: nucleus;nucleoplasm;CCAAT-binding factor complex;protein-DNA complex;RNA polymerase II transcription factor complex
Molecular function: RNA polymerase II proximal promoter sequence-specific DNA binding;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