GeneBe

NPAT

nuclear protein, coactivator of histone transcription

Basic information

Region (hg38): 11:108155280-108222638

Links

ENSG00000149308 ∙ NCBI:4863 ∙ OMIM:601448 ∙ HGNC:7896 ∙ Uniprot:Q14207 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

  • colorectal cancer (Limited), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Nodular lymphocyte predominant Hodgkin lymphoma, familialADOncologicIndividuals have been described as being at risk of nodular lymphocyte predominant Hodgkin lymphoma, and awareness may allow early disease detection and managamentOncologic21562039; 21778346

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the NPAT gene.

  • not_specified (2087 variants)
  • not_provided (451 variants)
  • NPAT-related_disorder (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NPAT gene is commonly pathogenic or not. These statistics are base on transcript: NM_000002519.3. 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.

EffectPLPVUSLBBSum
synonymous
2
clinvar
667
clinvar
 669
missense
1455
clinvar
78
clinvar
4
clinvar
 1537
nonsense
1
clinvar
 1
start loss
0
frameshift
4
clinvar
 4
splice donor/acceptor (+/-2bp)
3
clinvar
 3
Total 0 0 1465 745 4
Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
NPATprotein_codingprotein_codingENST00000278612 1865428
pLI Probability
LOF Intolerant 		pRec Probability
LOF Recessive 		Individuals with
no LOFs 		Individuals with
Homozygous LOFs 		Individuals with
Heterozygous LOFs 		Defined p
0.2820.7181247470491247960.000196
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense-0.1467267151.020.00003569345
Missense in Polyphen165202.40.815222754
Synonymous-0.2642622571.020.00001312807
Loss of Function5.351356.40.2310.00000275760

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0002160.000216
Ashkenazi Jewish0.0008080.000795
East Asian0.0002220.000223
Finnish0.00004640.0000464
European (Non-Finnish)0.0001860.000185
Middle Eastern0.0002220.000223
South Asian0.0002290.000229
Other0.0004980.000495

dbNSFP

Source: dbNSFP

Function
FUNCTION: Required for progression through the G1 and S phases of the cell cycle and for S phase entry. Activates transcription of the histone H2A, histone H2B, histone H3 and histone H4 genes in conjunction with MIZF. Also positively regulates the ATM, MIZF and PRKDC promoters. Transcriptional activation may be accomplished at least in part by the recruitment of the NuA4 histone acetyltransferase (HAT) complex to target gene promoters. {ECO:0000269|PubMed:10995386, ECO:0000269|PubMed:10995387, ECO:0000269|PubMed:12665581, ECO:0000269|PubMed:12724424, ECO:0000269|PubMed:14585971, ECO:0000269|PubMed:14612403, ECO:0000269|PubMed:15555599, ECO:0000269|PubMed:15988025, ECO:0000269|PubMed:16131487, ECO:0000269|PubMed:17163457, ECO:0000269|PubMed:17826007, ECO:0000269|PubMed:17967892, ECO:0000269|PubMed:17974976, ECO:0000269|PubMed:9472014}.;
Pathway
Retinoblastoma (RB) in Cancer (Consensus)

Recessive Scores

pRec
0.258

Intolerance Scores

loftool
0.642
rvis_EVS
0.63
rvis_percentile_EVS
83.58

Haploinsufficiency Scores

pHI
0.927
hipred
Y
hipred_score
0.637
ghis
0.587

Essentials

essential_gene_CRISPR
E
essential_gene_CRISPR2
E
essential_gene_gene_trap
E
gene_indispensability_pred
E
gene_indispensability_score
0.902

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Npat
Phenotype
growth/size/body region phenotype; endocrine/exocrine gland phenotype; homeostasis/metabolism phenotype; muscle phenotype; vision/eye phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); 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); reproductive system phenotype; embryo phenotype; respiratory system phenotype; immune system phenotype; renal/urinary system phenotype; skeleton phenotype; digestive/alimentary phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); limbs/digits/tail phenotype;

Gene ontology

Biological process
regulation of transcription involved in G1/S transition of mitotic cell cycle;regulation of gene expression;positive regulation of transcription, DNA-templated;negative regulation of nucleic acid-templated transcription
Cellular component
nucleus;nucleoplasm;cytoplasm;Cajal body;Gemini of coiled bodies
Molecular function
transcription coactivator activity;transcription corepressor activity;protein binding;protein C-terminus binding;protein N-terminus binding