NAP1L3

nucleosome assembly protein 1 like 3

Basic information

Region (hg38): X:93670930-93673578

Links

ENSG00000186310 ∙ NCBI:4675 ∙ OMIM:300117 ∙ HGNC:7639 ∙ Uniprot:Q99457 ∙ 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 NAP1L3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NAP1L3 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			28			28
nonsense						0
start loss						0
frameshift						0
inframe indel				1	1	2
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	28	2	1

Variants in NAP1L3

This is a list of pathogenic ClinVar variants found in the NAP1L3 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-93671788-T-C		not specified	Uncertain significance (Dec 19, 2022)
X-93671848-C-T		not specified	Uncertain significance (Jan 09, 2025)
X-93671889-T-A		not specified	Uncertain significance (Jan 09, 2023)
X-93671898-C-T			Likely benign (Apr 01, 2022)
X-93671927-C-A		not specified	Uncertain significance (Mar 14, 2023)
X-93671935-C-G		not specified	Uncertain significance (Aug 02, 2023)
X-93671957-T-C		not specified	Uncertain significance (Jun 07, 2023)
X-93671995-G-C		Abnormality of neuronal migration	Benign (Oct 31, 2014)
X-93671996-C-T		not specified	Uncertain significance (Dec 26, 2023)
X-93672002-G-A		not specified	Uncertain significance (Aug 01, 2024)
X-93672064-A-C		not specified	Uncertain significance (Feb 12, 2025)
X-93672191-C-T		not specified	Uncertain significance (Aug 04, 2024)
X-93672201-G-T		not specified	Uncertain significance (Jan 26, 2022)
X-93672242-T-A		not specified	Uncertain significance (Oct 06, 2023)
X-93672279-A-T		not specified	Uncertain significance (Dec 10, 2024)
X-93672283-G-A		not specified	Uncertain significance (Feb 11, 2022)
X-93672311-A-G		not specified	Uncertain significance (May 24, 2023)
X-93672390-T-G		not specified	Uncertain significance (Feb 02, 2025)
X-93672475-A-G		not specified	Uncertain significance (Nov 17, 2022)
X-93672481-G-T		not specified	Uncertain significance (Dec 20, 2023)
X-93672559-T-G		not specified	Uncertain significance (Oct 11, 2024)
X-93672608-C-T		not specified	Uncertain significance (Jul 19, 2023)
X-93672778-T-C		not specified	Uncertain significance (Dec 19, 2022)
X-93672802-T-A		not specified	Uncertain significance (Apr 13, 2022)
X-93672833-T-C		not specified	Uncertain significance (Aug 12, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NAP1L3	protein_coding	protein_coding	ENST00000373079	1	2639

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0879	0.875	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.492	160	179	0.896	0.0000116	3396
Missense in Polyphen		46	57.225	0.80384		1141
Synonymous	0.875	55	63.9	0.861	0.00000421	908
Loss of Function	1.78	3	8.64	0.347	6.26e-7	185

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

Recessive Scores

• pRec: 0.0789

Intolerance Scores

• loftool: 0.279
• rvis_EVS: 0.13
• rvis_percentile_EVS: 63.2

Haploinsufficiency Scores

• pHI: 0.318
• hipred: N
• hipred_score: 0.184
• ghis: 0.468

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.250

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nap1l3

Gene ontology

• Biological process: nucleosome assembly
• Cellular component: nucleus