NAP1L4

nucleosome assembly protein 1 like 4, the group of Small nucleolar RNA protein coding host genes

Basic information

Region (hg38): 11:2944431-2992377

Links

ENSG00000205531 ∙ NCBI:4676 ∙ OMIM:601651 ∙ HGNC:7640 ∙ Uniprot:Q99733 ∙ 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 NAP1L4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NAP1L4 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			22	2		24
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	22	2	1

Variants in NAP1L4

This is a list of pathogenic ClinVar variants found in the NAP1L4 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-2951309-C-G		not specified	Uncertain significance (Nov 17, 2023)
11-2954621-G-A		not specified	Uncertain significance (Nov 07, 2022)
11-2955751-T-C		not specified	Uncertain significance (Mar 25, 2024)
11-2955763-G-A		not specified	Uncertain significance (Jun 17, 2024)
11-2958410-T-C		not specified	Likely benign (Dec 27, 2022)
11-2958434-T-A		not specified	Uncertain significance (Sep 15, 2021)
11-2958449-G-A		not specified	Uncertain significance (Dec 01, 2022)
11-2958537-T-C		not specified	Uncertain significance (Mar 29, 2022)
11-2959890-T-A		not specified	Uncertain significance (May 29, 2024)
11-2959891-G-C		not specified	Uncertain significance (Oct 06, 2021)
11-2964682-T-C		not specified	Uncertain significance (May 05, 2023)
11-2964738-G-A		not specified	Uncertain significance (Dec 18, 2023)
11-2969816-C-T		not specified	Uncertain significance (Sep 17, 2021)
11-2969836-G-C		not specified	Uncertain significance (Jun 06, 2023)
11-2969841-T-C		not specified	Uncertain significance (Aug 13, 2021)
11-2969888-G-A		not specified	Uncertain significance (Sep 26, 2023)
11-2971471-T-C		not specified	Uncertain significance (Jun 29, 2022)
11-2971473-T-C		not specified	Uncertain significance (Jul 19, 2023)
11-2971497-T-C		not specified	Uncertain significance (Jan 23, 2024)
11-2971517-G-A			Benign (Jul 21, 2018)
11-2972179-T-C		not specified	Uncertain significance (Feb 23, 2023)
11-2972236-T-C		not specified	Uncertain significance (May 31, 2023)
11-2976031-T-C		not specified	Uncertain significance (Oct 12, 2022)
11-2976066-C-T		not specified	Uncertain significance (Jun 24, 2022)
11-2976090-C-T		not specified	Likely benign (Aug 02, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NAP1L4	protein_coding	protein_coding	ENST00000380542	14	47941

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.771	0.229	124652	0	142	124794	0.000569

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.722	177	206	0.859	0.0000111	2502
Missense in Polyphen		38	71.327	0.53276		925
Synonymous	0.335	72	75.7	0.951	0.00000463	641
Loss of Function	3.91	5	26.9	0.186	0.00000145	319

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000297	0.000297
Ashkenazi Jewish	0.0106	0.0107
East Asian	0.00	0.00
Finnish	0.0000464	0.0000464
European (Non-Finnish)	0.000159	0.000159
Middle Eastern	0.00	0.00
South Asian	0.0000654	0.0000654
Other	0.000826	0.000825

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Acts as histone chaperone in nucleosome assembly. {ECO:0000269|PubMed:9325046}.

Recessive Scores

• pRec: 0.109

Intolerance Scores

• loftool: 0.223
• rvis_EVS: -0.16
• rvis_percentile_EVS: 41.91

Haploinsufficiency Scores

• pHI: 0.455
• hipred: Y
• hipred_score: 0.530
• ghis: 0.595

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.893

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nap1l4

Gene ontology

• Biological process: nucleosome assembly
• Cellular component: nucleus;cytoplasm
• Molecular function: RNA binding;protein binding;nucleosome binding;unfolded protein binding