LENG1

leukocyte receptor cluster member 1, the group of Spliceosomal C complex|Spliceosomal P complex

Basic information

Region (hg38): 19:54155161-54159721

Links

ENSG00000105617 ∙ NCBI:79165 ∙ ∙ HGNC:15502 ∙ Uniprot:Q96BZ8 ∙ 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 LENG1 gene.

• not_specified (55 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LENG1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000024316.3. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			1			1
missense			55	2		57
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			3			3
Total	0	0	59	2	0

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LENG1	protein_coding	protein_coding	ENST00000222224	4	4722

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.58e-10	0.0317	125675	0	73	125748	0.000290

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.16	213	170	1.25	0.0000114	1663
Missense in Polyphen		83	63.573	1.3056		634
Synonymous	-1.88	85	65.6	1.30	0.00000360	562
Loss of Function	-0.485	14	12.2	1.15	8.31e-7	121

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000645	0.000635
Ashkenazi Jewish	0.00	0.00
East Asian	0.000110	0.000109
Finnish	0.000140	0.000139
European (Non-Finnish)	0.000415	0.000404
Middle Eastern	0.000110	0.000109
South Asian	0.000262	0.000261
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0850

Intolerance Scores

• loftool: 0.880
• rvis_EVS: 0.06
• rvis_percentile_EVS: 58.74

Haploinsufficiency Scores

• pHI: 0.536
• hipred: N
• hipred_score: 0.144
• ghis: 0.463

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: N
• gene_indispensability_score: 0.204

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Leng1

Gene ontology

• Biological process: biological_process
• Cellular component: cellular_component
• Molecular function: molecular_function;protein binding