LUC7L

LUC7 like

Basic information

Region (hg38): 16:188969-229463

Links

ENSG00000007392 ∙ NCBI:55692 ∙ OMIM:607782 ∙ HGNC:6723 ∙ Uniprot:Q9NQ29 ∙ 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 LUC7L gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LUC7L 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				2		2
missense			19	1	1	21
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	19	3	1

Variants in LUC7L

This is a list of pathogenic ClinVar variants found in the LUC7L region.

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

Position	Type	Phenotype	Significance	ClinVar
16-189203-T-C		not specified	Uncertain significance (Mar 22, 2023)
16-189233-G-A		not specified	Uncertain significance (Mar 01, 2024)
16-189242-T-C		not specified	Uncertain significance (May 14, 2024)
16-189271-T-G		not specified	Uncertain significance (Aug 04, 2023)
16-189308-A-C		not specified	Uncertain significance (Jul 15, 2021)
16-189322-G-A		not specified	Uncertain significance (May 31, 2023)
16-189977-G-A		not specified	Uncertain significance (Jun 18, 2021)
16-189983-C-T		not specified	Uncertain significance (Jan 16, 2024)
16-190001-C-T		LUC7L-related disorder	Likely benign (May 22, 2023)
16-190002-G-A		not specified	Uncertain significance (Jun 03, 2024)
16-190004-T-C		LUC7L-related disorder	Benign (Apr 30, 2019)
16-190023-G-A		not specified	Uncertain significance (Jul 15, 2021)
16-190050-T-C		not specified	Uncertain significance (Feb 05, 2024)
16-190088-C-T		not specified	Uncertain significance (Aug 17, 2022)
16-192930-C-T		not specified	Uncertain significance (Jan 31, 2022)
16-193003-C-T		not specified	Uncertain significance (Nov 21, 2023)
16-199131-C-T		LUC7L-related disorder	Likely benign (Jun 21, 2019)
16-206044-A-G		not specified	Uncertain significance (Jan 03, 2024)
16-206066-C-T		not specified	Uncertain significance (Oct 12, 2021)
16-206088-C-A		not specified	Uncertain significance (Jan 30, 2024)
16-208084-A-T		LUC7L-related disorder	Likely benign (Dec 20, 2019)
16-208107-C-G		not specified	Uncertain significance (Mar 31, 2024)
16-208163-A-G		not specified	Uncertain significance (Jan 04, 2022)
16-220651-C-A		not specified	Uncertain significance (Feb 05, 2024)
16-220675-C-T		not specified	Uncertain significance (Oct 26, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LUC7L	protein_coding	protein_coding	ENST00000293872	10	40495

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.470	0.530	125737	0	11	125748	0.0000437

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.88	165	248	0.664	0.0000179	2398
Missense in Polyphen		34	85.756	0.39647		909
Synonymous	0.0613	86	86.7	0.992	0.00000516	721
Loss of Function	3.51	5	23.3	0.215	0.00000150	248

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000181	0.000181
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000545	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000441	0.0000439
Middle Eastern	0.0000545	0.0000544
South Asian	0.0000330	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May bind to RNA via its Arg/Ser-rich domain. {ECO:0000269|PubMed:11170747}.

Recessive Scores

• pRec: 0.0856

Intolerance Scores

• loftool: 0.204
• rvis_EVS: 0.04
• rvis_percentile_EVS: 57.15

Haploinsufficiency Scores

• pHI: 0.539
• hipred: Y
• hipred_score: 0.793
• ghis: 0.498

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.925

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Luc7l
• Phenotype: normal phenotype

Gene ontology

• Biological process: mRNA splice site selection;negative regulation of striated muscle tissue development
• Cellular component: U1 snRNP;U2-type prespliceosome
• Molecular function: mRNA binding;protein binding;identical protein binding;RS domain binding