LUC7L3

LUC7 like 3 pre-mRNA splicing factor

Basic information

Region (hg38): 17:50719565-50756219

Links

ENSG00000108848 ∙ NCBI:51747 ∙ OMIM:609434 ∙ HGNC:24309 ∙ Uniprot:O95232 ∙ 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 LUC7L3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LUC7L3 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					1	1
missense			22			22
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	22	0	1

Variants in LUC7L3

This is a list of pathogenic ClinVar variants found in the LUC7L3 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-50741141-G-A			Benign (Dec 31, 2019)
17-50741187-C-T		not specified	Uncertain significance (Nov 10, 2022)
17-50741239-C-T		not specified	Uncertain significance (Mar 28, 2024)
17-50743747-G-T		not specified	Uncertain significance (Dec 21, 2023)
17-50745753-C-A		not specified	Uncertain significance (Oct 26, 2022)
17-50745753-C-T		not specified	Uncertain significance (Jul 05, 2024)
17-50745879-C-T		not specified	Uncertain significance (Oct 09, 2024)
17-50745891-A-G		not specified	Uncertain significance (Apr 19, 2024)
17-50745900-A-G		not specified	Uncertain significance (Jun 05, 2024)
17-50745996-C-T		not specified	Uncertain significance (Jan 18, 2023)
17-50746551-T-A		not specified	Uncertain significance (Sep 27, 2022)
17-50746571-A-T		not specified	Uncertain significance (Aug 09, 2021)
17-50746574-A-G		not specified	Uncertain significance (Jan 17, 2025)
17-50746606-C-T		not specified	Uncertain significance (Nov 19, 2022)
17-50746613-G-A		not specified	Uncertain significance (Jul 20, 2021)
17-50746636-C-G		not specified	Uncertain significance (Nov 08, 2024)
17-50746661-A-G		not specified	Uncertain significance (Oct 02, 2023)
17-50746666-C-T		not specified	Uncertain significance (Feb 02, 2022)
17-50746673-G-C		not specified	Uncertain significance (Feb 28, 2025)
17-50750527-A-T		not specified	Uncertain significance (Dec 04, 2024)
17-50750567-A-G		not specified	Uncertain significance (Sep 08, 2024)
17-50750575-A-C		not specified	Uncertain significance (Aug 27, 2024)
17-50750580-A-C		not specified	Uncertain significance (Mar 30, 2024)
17-50750627-A-G		not specified	Uncertain significance (Jun 25, 2024)
17-50750657-A-G		not specified	Uncertain significance (Jun 12, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LUC7L3	protein_coding	protein_coding	ENST00000505658	10	36670

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.00000653	125736	0	3	125739	0.0000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.58	127	239	0.530	0.0000143	2824
Missense in Polyphen		1	2.6459	0.37794		37
Synonymous	0.735	71	79.3	0.895	0.00000398	764
Loss of Function	5.36	0	33.5	0.00	0.00000261	343

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000281	0.0000264
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Binds cAMP regulatory element DNA sequence. May play a role in RNA splicing. {ECO:0000269|PubMed:16462885}.

Intolerance Scores

• loftool: 0.588
• rvis_EVS: 0.02
• rvis_percentile_EVS: 55.22

Haploinsufficiency Scores

• hipred: Y
• hipred_score: 0.729
• ghis: 0.633

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.731

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Luc7l3

Gene ontology

• Biological process: mRNA splice site selection;RNA splicing
• Cellular component: nucleus;nucleoplasm;U1 snRNP;nuclear speck;U2-type prespliceosome
• Molecular function: DNA binding;RNA binding;mRNA binding;protein binding