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.

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.

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			23	2		25
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding		1	3	5		9
Total	0	1	26	7	0

Variants in LENG1

This is a list of pathogenic ClinVar variants found in the LENG1 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-54155291-G-A			Likely benign (Dec 09, 2022)
19-54155300-C-G		CNOT3-related disorder	Uncertain significance (Feb 08, 2024)
19-54155302-C-T			Benign/Likely benign (Jan 01, 2023)
19-54155314-C-G			Likely benign (Aug 25, 2022)
19-54155326-T-C			Likely benign (Jan 13, 2023)
19-54155349-G-A			Uncertain significance (Nov 18, 2021)
19-54155354-A-G		Intellectual developmental disorder with speech delay, autism, and dysmorphic facies	Likely pathogenic (Jun 07, 2023)
19-54155377-C-A			Uncertain significance (Oct 31, 2023)
19-54155394-G-C		Inborn genetic diseases	Uncertain significance (Mar 29, 2024)
19-54155412-G-A		CNOT3-related disorder	Likely benign (Apr 11, 2019)
19-54155737-G-A		not specified	Uncertain significance (Apr 28, 2022)
19-54155738-G-C		not specified	Uncertain significance (May 26, 2023)
19-54155758-C-T		not specified	Uncertain significance (Jan 30, 2024)
19-54155795-G-A		not specified	Uncertain significance (Aug 04, 2022)
19-54155801-G-A		not specified	Uncertain significance (May 24, 2023)
19-54155814-G-T		not specified	Likely benign (Feb 05, 2024)
19-54155832-C-A		not specified	Uncertain significance (May 26, 2024)
19-54155845-C-T		not specified	Uncertain significance (Nov 10, 2022)
19-54155858-G-A		not specified	Uncertain significance (Jul 25, 2023)
19-54155908-C-T		not specified	Uncertain significance (Aug 16, 2021)
19-54155909-G-A		not specified	Uncertain significance (Mar 24, 2023)
19-54156824-C-T		not specified	Uncertain significance (Oct 03, 2023)
19-54156866-G-A		not specified	Uncertain significance (Oct 13, 2023)
19-54156878-G-C		not specified	Uncertain significance (Feb 15, 2023)
19-54156881-G-A		not specified	Uncertain significance (Jan 26, 2022)

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