LNP1

leukemia NUP98 fusion partner 1

Basic information

Region (hg38): 3:100401532-100456319

Links

ENSG00000206535 ∙ NCBI:348801 ∙ ∙ HGNC:28014 ∙ Uniprot:A1A4G5 ∙ 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 LNP1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LNP1 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			12			12
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	12	0	0

Variants in LNP1

This is a list of pathogenic ClinVar variants found in the LNP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-100429787-T-A		not specified	Uncertain significance (Mar 19, 2024)
3-100429811-G-A		not specified	Uncertain significance (Dec 16, 2022)
3-100429835-C-T		not specified	Uncertain significance (Dec 27, 2022)
3-100429854-C-T		not specified	Uncertain significance (Dec 21, 2022)
3-100451757-T-TGGAATTCCGATGCCGATCGTCTGACCGTCTTCCTAGAAGGCATTCTCATGAGGACCA		Neurodevelopmental disorder with epilepsy and hypoplasia of the corpus callosum	Benign (May 30, 2022)
3-100451766-G-T		not specified	Uncertain significance (Dec 14, 2021)
3-100451807-T-G		not specified	Uncertain significance (Jul 25, 2023)
3-100451848-G-C		not specified	Uncertain significance (Dec 07, 2021)
3-100451871-A-T		not specified	Uncertain significance (Apr 17, 2023)
3-100451897-C-T		not specified	Uncertain significance (Aug 14, 2023)
3-100451912-G-T		not specified	Uncertain significance (Nov 07, 2023)
3-100451935-C-T		not specified	Uncertain significance (Aug 08, 2022)
3-100455847-T-C		not specified	Uncertain significance (Jun 30, 2022)
3-100455849-G-A		not specified	Uncertain significance (Dec 19, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LNP1	protein_coding	protein_coding	ENST00000383693	3	55127

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000443	0.235	124782	0	17	124799	0.0000681

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.364	91	101	0.898	0.00000568	1174
Missense in Polyphen		24	25.566	0.93876		355
Synonymous	0.495	30	33.6	0.892	0.00000155	313
Loss of Function	-0.0866	8	7.74	1.03	4.78e-7	84

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000409	0.000383
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000464	0.0000464
European (Non-Finnish)	0.0000444	0.0000441
Middle Eastern	0.00	0.00
South Asian	0.0000993	0.0000980
Other	0.000165	0.000165

dbNSFP

Source: dbNSFP

• Disease: DISEASE: Note=A chromosomal aberration involving LNP1 is found in a form of T-cell acute lymphoblastic leukemia (T-ALL). Translocation t(3;11)(q12.2;p15.4) with NUP98. {ECO:0000269|PubMed:16467868}.

Recessive Scores

• pRec: 0.100

Intolerance Scores

• loftool: 0.453
• rvis_EVS: 0.04
• rvis_percentile_EVS: 56.64

Haploinsufficiency Scores

• pHI: 0.169
• hipred: N
• hipred_score: 0.184
• ghis: 0.525

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.205

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lnp1