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

Transcripts

Transcript IDs starting with ENST are treated as Ensembl, all others as RefSeq. Showing 4 of 8.

Transcript ID	Protein ID	Coding exons	MANE Select	MANE Plus Clinical
NM_002519.3	NP_002510.2	18	yes	-
ENST00000278612.9	ENSP00000278612.8	18	yes	-
NM_001321307.1	NP_001308236.1	18	-	-
ENST00000527296.1	ENSP00000436510.1	2	-	-

Phenotypes

GenCC

Source: genCC

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

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Nodular lymphocyte predominant Hodgkin lymphoma, familial	AD	Oncologic	Individuals have been described as being at risk of nodular lymphocyte predominant Hodgkin lymphoma, and awareness may allow early disease detection and managament	Oncologic	21562039; 21778346

ClinVar

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

• not_specified (2093 variants)
• not_provided (568 variants)
• NPAT-related_disorder (2 variants)
• Familial_colorectal_cancer_type_X (1 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_002519.3. 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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			6	672		678
missense			1483	78	4	1565
nonsense			3			3
start loss						0
frameshift			7			7
splice donor/acceptor (+/-2bp)			7			7
Total	0	0	1506	750	4

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NPAT	protein_coding	protein_coding	ENST00000278612	18	65428

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
		124747	0	49	124796	0.000196

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.146	726	715	1.02	0.0000356	9345
Missense in Polyphen		165	202.4	0.81522		2754
Synonymous	-0.264	262	257	1.02	0.0000131	2807
Loss of Function	5.35	13	56.4	0.231	0.00000275	760

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000216	0.000216
Ashkenazi Jewish	0.000808	0.000795
East Asian	0.000222	0.000223
Finnish	0.0000464	0.0000464
European (Non-Finnish)	0.000186	0.000185
Middle Eastern	0.000222	0.000223
South Asian	0.000229	0.000229
Other	0.000498	0.000495

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

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

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

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