LUC7L3

protein-coding

LUC7 like 3 pre-mRNA splicing factor

Gene summary

This gene encodes a protein with an N-terminal half that contains cysteine/histidine motifs and leucine zipper-like repeats, and the C-terminal half is rich in arginine and glutamate residues (RE domain) and arginine and serine residues (RS domain). This protein localizes with a speckled pattern in the nucleus, and could be involved in the formation of splicesome via the RE and RS domains. Two alternatively spliced transcript variants encoding the same protein have been found for this gene. [provided by RefSeq, Aug 2009]

MANE transcript

NM_016424.5

Inheritance

—

ClinVar variants

U:35B:1

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0

Max pathogenic AF

—

Genomic locus

chr17:50,719,565-50,756,219

External References & Databases

Ensembl (ENSG00000108848)

Transcript & Mutation Effects

hg38 • Region Span ~36.7 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to LUC7L3 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 31

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_016424.5. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			2 clinvar		1 clinvar	3
missense			32 clinvar			32
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	35	0	1	36

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 37 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_016424.5	RefSeq	NP_057508.2	10	MANE Select
ENST00000505658.6	Ensembl	ENSP00000425092.1	10	MANE Select
NM_001330330.2	RefSeq	NP_001317259.1	11	Standard
NM_006107.4	RefSeq	NP_006098.2	10	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

mRNA splice site selection
RNA splicing

Molecular Function

DNA binding
RNA binding
mRNA binding
protein binding

Cellular Component

nucleus
nucleoplasm
U1 snRNP
nuclear speck
U2-type prespliceosome

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000505658
Coding exons: 10
Length: 36670
Individuals with no LoFs: 125736
Homozygous LoFs: 0
Heterozygous LoFs: 3
Defined: 125739
p: 0.0000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.58	127	239	0.530	0.0000143	2824
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000028	0.000026	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): E
Essential (CRISPR2): E
Essential (gene trap): E
Indispensability pred.: E
Indispensability score: 0.731

Gene Damage Prediction

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