NAP1L1

nucleosome assembly protein 1 like 1

Basic information

Region (hg38): 12:76036585-76084735

Links

ENSG00000187109 ∙ NCBI:4673 ∙ OMIM:164060 ∙ HGNC:7637 ∙ Uniprot:P55209 ∙ 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 NAP1L1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NAP1L1 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		1
missense			15			15
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	15	1	0

Variants in NAP1L1

This is a list of pathogenic ClinVar variants found in the NAP1L1 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-76049214-C-G		not specified	Uncertain significance (Aug 01, 2023)
12-76049235-C-T		not specified	Uncertain significance (Sep 06, 2022)
12-76050533-C-A		not specified	Uncertain significance (Jan 22, 2024)
12-76050628-G-A		not specified	Uncertain significance (May 26, 2023)
12-76056074-T-C		not specified	Uncertain significance (Mar 01, 2023)
12-76056118-T-A		not specified	Uncertain significance (Jun 13, 2024)
12-76056119-C-T		not specified	Uncertain significance (Oct 17, 2023)
12-76056138-C-A		not specified	Uncertain significance (May 23, 2023)
12-76056145-T-C		not specified	Uncertain significance (Nov 21, 2023)
12-76060269-C-T		not specified	Uncertain significance (Dec 28, 2023)
12-76067443-T-C		not specified	Uncertain significance (Jul 12, 2022)
12-76067448-C-T		not specified	Uncertain significance (Aug 19, 2023)
12-76068915-G-A		not specified	Uncertain significance (Aug 06, 2021)
12-76068933-T-C		not specified	Uncertain significance (Mar 20, 2024)
12-76068940-T-C			Likely benign (Jul 31, 2018)
12-76068972-G-C		not specified	Uncertain significance (Apr 07, 2022)
12-76068987-G-C		not specified	Uncertain significance (Jun 29, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NAP1L1	protein_coding	protein_coding	ENST00000261182	14	40144

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.999	0.000589	125568	0	6	125574	0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.76	132	203	0.652	0.0000101	2631
Missense in Polyphen		8	39.893	0.20053		594
Synonymous	0.379	57	60.8	0.938	0.00000288	634
Loss of Function	4.53	1	25.8	0.0387	0.00000127	328

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000622	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000563	0.0000544
Finnish	0.0000473	0.0000462
European (Non-Finnish)	0.0000178	0.0000176
Middle Eastern	0.0000563	0.0000544
South Asian	0.0000336	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays a key role in the regulation of embryonic neurogenesis (By similarity). Promotes the proliferation of neural progenitors and inhibits neuronal differentiation during cortical development (By similarity). Regulates neurogenesis via the modulation of RASSF10; regulates RASSF10 expression by promoting SETD1A-mediated H3K4 methylation at the RASSF10 promoter (By similarity). {ECO:0000250|UniProtKB:P28656}.

Recessive Scores

• pRec: 0.183

Intolerance Scores

• loftool: 0.641
• rvis_EVS: -0.25
• rvis_percentile_EVS: 35.42

Haploinsufficiency Scores

• pHI: 0.997
• hipred: Y
• hipred_score: 0.818
• ghis: 0.669

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: H
• gene_indispensability_pred: E
• gene_indispensability_score: 0.952

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nap1l1
• 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); 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)

Gene ontology

• Biological process: DNA replication;nucleosome assembly;positive regulation of cell population proliferation;positive regulation of neurogenesis;positive regulation of neural precursor cell proliferation
• Cellular component: nucleus;cytoplasm;membrane;melanosome
• Molecular function: RNA binding;protein binding