SLU7

protein-coding

SLU7 homolog, splicing factor, the group of Spliceosomal C complex|U11 small nuclear ribonucleoprotein|Spliceosomal P complex|NTC associated proteins

Gene summary

Pre-mRNA splicing occurs in two sequential transesterification steps. The protein encoded by this gene is a splicing factor that has been found to be essential during the second catalytic step in the pre-mRNA splicing process. It associates with the spliceosome and contains a zinc knuckle motif that is found in other splicing factors and is involved in protein-nucleic acid and protein-protein interactions. [provided by RefSeq, Jul 2008]

MANE transcript

NM_006425.5

Inheritance

—

ClinVar variants

U:57B:2

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.52

Max pathogenic AF

—

Genomic locus

chr5:160,401,641-160,421,711

External References & Databases

Ensembl (ENSG00000164609)

Transcript & Mutation Effects

hg38 • Region Span ~20.1 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 SLU7 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 49

not providedTotal: 4

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_006425.5. 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			2
missense			48 clinvar	1 clinvar	1 clinvar	50
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			7 clinvar			7
Total	0	0	57	1	1	59

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 24 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_006425.5	RefSeq	NP_006416.3	15	MANE Select
ENST00000297151.9	Ensembl	ENSP00000297151.4	15	MANE Select
NM_001364517.2	RefSeq	NP_001351446.1	16	Standard
NM_001364518.2	RefSeq	NP_001351447.1	15	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Spliceosome - Homo sapiens (human)
Gene expression (Transcription)
RNA Polymerase II Transcription
Metabolism of RNA
Cleavage of Growing Transcript in the Termination Region

Biological Process

RNA splicing, via transesterification reactions
alternative mRNA splicing, via spliceosome
mRNA 3'-splice site recognition
mRNA splicing, via spliceosome
RNA export from nucleus

Molecular Function

second spliceosomal transesterification activity
protein binding
zinc ion binding
pre-mRNA 3'-splice site binding

Cellular Component

nucleus
nucleoplasm
spliceosomal complex
cytoplasm
cytosol

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000297151
Coding exons: 15
Length: 20071
Individuals with no LoFs: 125691
Homozygous LoFs: 0
Heterozygous LoFs: 57
Defined: 125748
p: 0.000227

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.99	203	300	0.677	0.0000147	3893
Missense (PolyPhen)		53	118.86	0.44592		1550
Synonymous	1.27	82	98.0	0.837	0.00000453	981
Loss of Function	2.79	21	40.1	0.524	0.00000233	487

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00037	0.00037	rare
Latino/Admixed American	0.00021	0.00020	rare
Ashkenazi Jewish	0.00063	0.00060	rare
East Asian	0.00011	0.00011	rare
Finnish	0.00014	0.00014	rare
European (Non-Finnish)	0.00019	0.00018	rare
South Asian	0.00036	0.00036	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Participates in the second catalytic step of pre-mRNA splicing, when the free hydroxyl group of exon I attacks the 3'- splice site to generate spliced mRNA and the excised lariat intron. Required for holding exon 1 properly in the spliceosome and for correct AG identification when more than one possible AG exists in 3'-splicing site region. May be involved in the activation of proximal AG. Probably also involved in alternative splicing regulation. {ECO:0000269|PubMed:10197984, ECO:0000269|PubMed:10647016, ECO:0000269|PubMed:12764196, ECO:0000269|PubMed:15728250}.;

Recessive Scores

pRec: 0.125

Intolerance Scores

LoFtool: 0.892
RVIS EVS: -0.09
RVIS percentile EVS: 46.92

Essentials

Essential (CRISPR): N
Essential (CRISPR2): E
Essential (gene trap): E
Indispensability pred.: E
Indispensability score: 0.681

Gene Damage Prediction

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