LUC7L2

protein-coding

LUC7 like 2, pre-mRNA splicing factor

Gene summary

This gene encodes a protein that contains a C2H2-type zinc finger, coiled-coil region and arginine, serine-rich (RS) domain. A similar protein in mouse interacts with sodium channel modifier 1, and the encoded protein may be involved in the recognition of non-consensus splice donor sites in association with the U1 snRNP spliceosomal subunit. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Sep 2011]

MANE transcript

NM_016019.5

Inheritance

—

ClinVar variants

U:31

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.28

Max pathogenic AF

—

Genomic locus

chr7:139,340,359-139,423,457

External References & Databases

Ensembl (ENSG00000146963)

Transcript & Mutation Effects

hg38 • Region Span ~83.1 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 LUC7L2 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 29

not providedTotal: 3

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_016019.5. 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			1 clinvar			1
missense			29 clinvar			29
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	31	0	0	31

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 57 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_016019.5	RefSeq	NP_057103.2	10	MANE Select
ENST00000354926.9	Ensembl	ENSP00000347005.4	10	MANE Select
NM_001244585.2	RefSeq	NP_001231514.1	10	Standard
NM_001270643.2	RefSeq	NP_001257572.1	10	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

mRNA splice site selection

Molecular Function

RNA binding
mRNA binding
protein binding
enzyme binding

Cellular Component

U1 snRNP
nuclear speck
U2-type prespliceosome

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000354926
Coding exons: 10
Length: 83094
Individuals with no LoFs: 124776
Homozygous LoFs: 0
Heterozygous LoFs: 15
Defined: 124791
p: 0.0000601

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.62	117	229	0.512	0.0000142	2560
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000059	0.000058	rare
Ashkenazi Jewish	0.00010	0.000099	rare
East Asian	0	0.0	absent
Finnish	0.000048	0.000046	rare
European (Non-Finnish)	0.00010	0.000088	rare
South Asian	0.000038	0.000033	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): E
Essential (CRISPR2): S
Indispensability pred.: E
Indispensability score: 0.998

Gene Damage Prediction

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