NPAT

nuclear protein, coactivator of histone transcription

Basic information

Region (hg38): 11:108157214-108222638

Links

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

Phenotypes

GenCC

Source: genCC

No genCC data.

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.

• Inborn genetic diseases (1537 variants)
• not provided (184 variants)
• not specified (47 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.

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			1	515		516
missense			1011	39	8	1058
nonsense			1			1
start loss						0
frameshift			1			1
inframe indel			5		1	6
splice donor/acceptor (+/-2bp)			1			1
splice region			3	7	1	11
non coding			7	15	6	28
Total	0	0	1027	569	15

Variants in NPAT

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

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

Position	Type	Phenotype	Significance	ClinVar
11-108157463-CTATATGA-C		not specified	Uncertain significance (Apr 01, 2019)
11-108157583-TTG-T		not specified	Uncertain significance (Dec 20, 2019)
11-108157851-C-G		not specified	Uncertain significance (Sep 20, 2019)
11-108157939-T-C		not specified	Likely benign (Nov 13, 2019)
11-108158003-T-C		not specified	Uncertain significance (Jul 01, 2019)
11-108158104-TAA-T		not specified	Benign (Nov 25, 2019)
11-108158572-G-A		not specified	Uncertain significance (Jan 17, 2018)
11-108158594-T-A		not specified	Uncertain significance (Apr 02, 2019)
11-108158947-C-T		not specified	Uncertain significance (Sep 27, 2023)
11-108158951-A-G		not specified	Likely benign (Jul 01, 2023)
11-108158957-C-T		not specified	Likely benign (Feb 27, 2023)
11-108158960-T-C		not specified	Likely benign (Dec 29, 2021)
11-108158963-T-C		not specified	Likely benign (Nov 16, 2023)
11-108158963-T-G		not specified	Uncertain significance (Feb 25, 2023)
11-108158968-A-G		not specified	Likely benign (Sep 28, 2023)
11-108158970-A-C		not specified	Uncertain significance (Mar 08, 2023)
11-108158973-T-C		not specified	Uncertain significance (Jun 16, 2023)
11-108158980-C-T		not specified	Uncertain significance (Jun 04, 2022)
11-108158983-C-T		not specified	Uncertain significance (Sep 17, 2023)
11-108158984-C-T		not specified	Uncertain significance (Nov 24, 2021)
11-108158995-G-T		not specified	Uncertain significance (Jul 29, 2021)
11-108159000-G-A		not specified	Uncertain significance (Sep 12, 2022)
11-108159001-A-C		not specified	Uncertain significance (Mar 12, 2023)
11-108159003-C-A		not specified	Uncertain significance (Oct 15, 2022)
11-108159003-C-G		not specified	Uncertain significance (Sep 20, 2022)

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
0.282	0.718	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

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

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

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