NAP1L2

nucleosome assembly protein 1 like 2

Basic information

Region (hg38): X:73212299-73214851

Links

ENSG00000186462 ∙ NCBI:4674 ∙ OMIM:300026 ∙ HGNC:7638 ∙ Uniprot:Q9ULW6 ∙ 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 NAP1L2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NAP1L2 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					2	2
missense			29	2		31
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	29	2	2

Variants in NAP1L2

This is a list of pathogenic ClinVar variants found in the NAP1L2 region.

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

Position	Type	Phenotype	Significance	ClinVar
X-73213255-A-T		not specified	Uncertain significance (Dec 03, 2024)
X-73213352-A-C		not specified	Uncertain significance (Aug 20, 2024)
X-73213361-C-T		not specified	Uncertain significance (Aug 20, 2024)
X-73213477-T-C		not specified	Uncertain significance (Jan 26, 2022)
X-73213487-T-G		not specified	Uncertain significance (Apr 20, 2024)
X-73213595-C-T		not specified	Uncertain significance (Oct 05, 2021)
X-73213739-C-G		not specified	Uncertain significance (Aug 02, 2021)
X-73213784-G-T		not specified	Uncertain significance (Dec 06, 2022)
X-73213817-C-A		not specified	Uncertain significance (Mar 16, 2024)
X-73213822-A-T		not specified	Uncertain significance (Jun 01, 2023)
X-73213831-T-C		not specified	Uncertain significance (May 07, 2024)
X-73213839-C-G		not specified	Likely benign (Sep 01, 2021)
X-73213893-G-T		not specified	Uncertain significance (Dec 19, 2022)
X-73213911-A-T		not specified	Uncertain significance (Mar 13, 2023)
X-73213916-C-T		not specified	Uncertain significance (Aug 14, 2024)
X-73213936-T-C		not specified	Uncertain significance (Jun 27, 2022)
X-73213937-A-T		not specified	Uncertain significance (Aug 20, 2024)
X-73213938-C-T		not specified	Uncertain significance (Feb 28, 2023)
X-73213947-A-G			Benign (Nov 24, 2017)
X-73213952-A-G		not specified	Uncertain significance (Nov 15, 2024)
X-73213953-C-A		not specified	Uncertain significance (Aug 17, 2021)
X-73213969-C-T		not specified	Likely benign (Nov 08, 2024)
X-73213985-A-G		Abnormality of neuronal migration	Uncertain significance (Oct 31, 2014)
X-73213996-C-A		not specified	Uncertain significance (May 15, 2023)
X-73214051-G-C		not specified	Uncertain significance (May 24, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NAP1L2	protein_coding	protein_coding	ENST00000373517	1	2550

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.781	0.218	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.102	162	166	0.978	0.0000112	3044
Missense in Polyphen		36	54.589	0.65948		1097
Synonymous	-2.13	83	61.7	1.35	0.00000413	845
Loss of Function	2.54	1	9.38	0.107	6.60e-7	222

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Acidic protein which may be involved in interactions with other proteins or DNA. {ECO:0000250}.

Recessive Scores

• pRec: 0.0995

Intolerance Scores

• loftool: 0.293
• rvis_EVS: -0.12
• rvis_percentile_EVS: 44.89

Haploinsufficiency Scores

• pHI: 0.567
• hipred: N
• hipred_score: 0.184
• ghis: 0.600

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.925

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nap1l2
• 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); embryo phenotype

Gene ontology

• Biological process: nucleosome assembly;positive regulation of neuron differentiation;positive regulation of histone H3-K14 acetylation;regulation of stem cell division;positive regulation of histone H3-K9 acetylation
• Cellular component: nucleus
• Molecular function: chromatin binding;protein binding;histone binding