GeneBe

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.

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.

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
10
clinvar
 10
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
0
Total 0 0 10 0 0

Variants in NFYA

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

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

Position Type Phenotype Significance ClinVar
6-41079123-A-G not specified Uncertain significance (Dec 06, 2021)2265034
6-41080855-G-C not specified Uncertain significance (Dec 07, 2022)2332308
6-41089584-G-C not specified Uncertain significance (Jan 19, 2025)3879374
6-41090271-A-G not specified Uncertain significance (Aug 31, 2022)2309849
6-41090279-G-C not specified Uncertain significance (Jan 23, 2025)3879373
6-41091626-G-A not specified Uncertain significance (Oct 20, 2023)3198851
6-41091638-G-A not specified Uncertain significance (Sep 08, 2023)2620871
6-41091675-A-G not specified Uncertain significance (Apr 22, 2024)3299593
6-41091684-G-C not specified Uncertain significance (Aug 31, 2022)2309850
6-41097357-G-A not specified Uncertain significance (Jun 28, 2022)3198861
6-41097365-C-G not specified Uncertain significance (Feb 22, 2023)2486987
6-41097402-G-C not specified Uncertain significance (May 27, 2022)2292017

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
NFYAprotein_codingprotein_codingENST00000341376 927032
pLI Probability
LOF Intolerant 		pRec Probability
LOF Recessive 		Individuals with
no LOFs 		Individuals with
Homozygous LOFs 		Individuals with
Heterozygous LOFs 		Defined p
0.1460.854125740081257480.0000318
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense2.78851940.4380.000009912241
Missense in Polyphen1352.7370.24651522
Synonymous-0.1757068.21.030.00000343706
Loss of Function3.32623.30.2580.00000119218

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.00006160.0000615
Ashkenazi Jewish0.000.00
East Asian0.00005440.0000544
Finnish0.000.00
European (Non-Finnish)0.00002640.0000264
Middle Eastern0.00005440.0000544
South Asian0.00006550.0000653
Other0.0001640.000163

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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