LUC7L2

LUC7 like 2, pre-mRNA splicing factor

Basic information

Region (hg38): 7:139340359-139423457

Links

ENSG00000146963 ∙ NCBI:51631 ∙ OMIM:613056 ∙ HGNC:21608 ∙ Uniprot:Q9Y383 ∙ 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 LUC7L2 gene.

• not_specified (26 variants)
• not_provided (4 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LUC7L2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000016019.5. 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						0
missense			26			26
nonsense						0
start loss						0
frameshift			1			1
splice donor/acceptor (+/-2bp)						0
Total	0	0	27	0	0

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LUC7L2	protein_coding	protein_coding	ENST00000354926	10	83094

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0553	0.945	124776	0	15	124791	0.0000601

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.62	117	229	0.512	0.0000142	2560
Missense in Polyphen		15	68.542	0.21884		890
Synonymous	1.21	57	69.8	0.816	0.00000325	714
Loss of Function	3.32	7	24.8	0.282	0.00000172	287

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000594	0.0000594
Ashkenazi Jewish	0.0000996	0.0000993
East Asian	0.00	0.00
Finnish	0.0000481	0.0000464
European (Non-Finnish)	0.000102	0.0000883
Middle Eastern	0.00	0.00
South Asian	0.0000378	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May bind to RNA via its Arg/Ser-rich domain.

Recessive Scores

• pRec: 0.121

Intolerance Scores

• rvis_EVS: 0.15
• rvis_percentile_EVS: 64.32

Haploinsufficiency Scores

• pHI: 0.445
• hipred: N
• hipred_score: 0.407
• ghis: 0.559

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: S
• gene_indispensability_pred: E
• gene_indispensability_score: 0.998

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Luc7l2

Gene ontology

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