NAP1L5

nucleosome assembly protein 1 like 5

Basic information

Region (hg38): 4:88695913-88697829

Links

ENSG00000177432 ∙ NCBI:266812 ∙ OMIM:612203 ∙ HGNC:19968 ∙ Uniprot:Q96NT1 ∙ 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 NAP1L5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NAP1L5 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						0
missense			20	1		21
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	20	1	0

Variants in NAP1L5

This is a list of pathogenic ClinVar variants found in the NAP1L5 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-88697251-T-A		not specified	Uncertain significance (Apr 25, 2022)
4-88697282-T-G		not specified	Uncertain significance (Aug 05, 2024)
4-88697312-T-G		not specified	Uncertain significance (Apr 27, 2024)
4-88697313-C-T		not specified	Uncertain significance (May 11, 2022)
4-88697316-C-T		not specified	Uncertain significance (Nov 07, 2024)
4-88697328-C-T			Likely benign (Aug 13, 2018)
4-88697330-T-C		not specified	Uncertain significance (Mar 01, 2023)
4-88697348-C-T		not specified	Uncertain significance (Sep 16, 2021)
4-88697349-C-T		not specified	Uncertain significance (Dec 27, 2023)
4-88697458-A-C		not specified	Uncertain significance (Oct 17, 2023)
4-88697555-T-C		not specified	Uncertain significance (Oct 12, 2021)
4-88697561-G-T		not specified	Uncertain significance (Nov 21, 2022)
4-88697562-G-A		not specified	Uncertain significance (Dec 22, 2023)
4-88697615-G-T		not specified	Uncertain significance (Aug 22, 2023)
4-88697654-C-T		not specified	Uncertain significance (Jan 04, 2024)
4-88697656-C-A		not specified	Uncertain significance (Nov 17, 2023)
4-88697670-C-G		not specified	Uncertain significance (Oct 17, 2023)
4-88697694-C-T		not specified	Uncertain significance (Jul 26, 2022)
4-88697702-G-A		not specified	Uncertain significance (Mar 20, 2023)
4-88697721-G-T		not specified	Uncertain significance (May 18, 2023)
4-88697722-C-A		not specified	Uncertain significance (May 18, 2023)
4-88697726-G-A		not specified	Uncertain significance (Aug 02, 2022)
4-88697730-G-T		not specified	Uncertain significance (Feb 27, 2024)
4-88697745-A-T		not specified	Uncertain significance (Dec 28, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NAP1L5	protein_coding	protein_coding	ENST00000323061	1	2321

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.693	0.291	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.393	100	112	0.895	0.00000612	1203
Missense in Polyphen		5	18.024	0.27741		232
Synonymous	-0.741	61	54.1	1.13	0.00000395	331
Loss of Function	1.82	0	3.87	0.00	2.60e-7	34

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: 0.110

Intolerance Scores

• loftool: 0.285
• rvis_EVS: -0.32
• rvis_percentile_EVS: 31.46

Haploinsufficiency Scores

• pHI: 0.350
• hipred: N
• hipred_score: 0.291
• ghis: 0.565

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.299

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nap1l5

Gene ontology

• Biological process: nucleosome assembly
• Cellular component: nucleus