LNP1

Gene

leukemia NUP98 fusion partner 1

Gene summary

No gene description available in the current model. Review primary literature for detailed gene function and characteristics.

MANE transcript

NM_001085451.2

Inheritance

—

ClinVar variants

U:26B:2

Top phenotype

Neurodevelopmental disorder with epilepsy and hypoplasia of the corpus callosum

gnomAD constraint

pLI —, LoF o/e 1.03

Max pathogenic AF

—

Genomic locus

chr3:100,401,532-100,456,319

External References & Databases

Ensembl (ENSG00000206535)

Transcript & Mutation Effects

hg38 • Region Span ~54.8 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to LNP1 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 22

not providedTotal: 1

Neurodevelopmental disorder with epilepsy and hypoplasia of the corpus callosumTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001085451.2. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous				1 clinvar		1
missense			24 clinvar			24
nonsense					1 clinvar	1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	26	1	1	28

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 17 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001085451.2	RefSeq	NP_001078920.1	3	MANE Select
ENST00000383693.8	Ensembl	ENSP00000373191.3	3	MANE Select
ENST00000466996.5	Ensembl	ENSP00000419213.1	2	Standard
ENST00000489752.1	Ensembl	ENSP00000417985.1	3	Standard

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000383693
Coding exons: 3
Length: 55127
Individuals with no LoFs: 124782
Homozygous LoFs: 0
Heterozygous LoFs: 17
Defined: 124799
p: 0.0000681

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.364	91	101	0.898	0.00000568	1174
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00035	0.00032	rare
Latino/Admixed American	0.000060	0.000058	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.000044	0.000044	rare
South Asian	0.000099	0.000098	rare
Other	0.00017	0.00016	rare

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.205

Gene Damage Prediction

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