SLU7

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

Basic information

Region (hg38): 5:160401641-160421711

Links

ENSG00000164609 ∙ NCBI:10569 ∙ OMIM:605974 ∙ HGNC:16939 ∙ Uniprot:O95391 ∙ 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 SLU7 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLU7 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						0
missense			19		1	20
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				2		2
non coding				1		1
Total	0	0	19	1	1

Variants in SLU7

This is a list of pathogenic ClinVar variants found in the SLU7 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-160403317-C-A		not specified	Uncertain significance (Jul 05, 2024)
5-160403388-T-C		not specified	Uncertain significance (Oct 29, 2024)
5-160403397-C-T		not specified	Uncertain significance (Apr 07, 2022)
5-160403442-C-T		not specified	Uncertain significance (Oct 28, 2024)
5-160403458-T-C		not specified	Uncertain significance (Dec 16, 2022)
5-160403463-G-A		not specified	Uncertain significance (Nov 21, 2023)
5-160404495-C-T		not specified	Uncertain significance (Aug 12, 2022)
5-160404519-T-G		not specified	Uncertain significance (Mar 03, 2022)
5-160404525-T-C		not specified	Uncertain significance (Dec 15, 2022)
5-160404540-A-G		not specified	Uncertain significance (Jan 03, 2024)
5-160404812-C-T		not specified	Uncertain significance (Sep 27, 2021)
5-160404847-C-T		not specified	Uncertain significance (Dec 20, 2021)
5-160405032-A-G		not specified	Likely benign (Oct 08, 2024)
5-160405125-C-T		not specified	Uncertain significance (Mar 21, 2023)
5-160406481-A-T		not specified	Uncertain significance (Oct 12, 2022)
5-160406482-T-C		not specified	Uncertain significance (May 25, 2022)
5-160406512-C-G		not specified	Uncertain significance (Dec 03, 2024)
5-160406514-A-G		not specified	Uncertain significance (Apr 18, 2023)
5-160406601-G-A		not specified	Uncertain significance (Dec 07, 2024)
5-160407477-T-A		not specified	Uncertain significance (May 04, 2022)
5-160407615-A-G		not specified	Uncertain significance (Apr 15, 2024)
5-160408454-C-A		not specified	Uncertain significance (Oct 29, 2021)
5-160408669-T-A		not specified	Uncertain significance (Jun 30, 2023)
5-160408683-G-T		not specified	Uncertain significance (Dec 13, 2021)
5-160412523-T-TAAAAAAAAA			Likely benign (Jan 12, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLU7	protein_coding	protein_coding	ENST00000297151	15	20071

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.63e-9	0.998	125691	0	57	125748	0.000227

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.99	203	300	0.677	0.0000147	3893
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000582	0.000578
Ashkenazi Jewish	0.000630	0.000595
East Asian	0.000109	0.000109
Finnish	0.000139	0.000139
European (Non-Finnish)	0.000187	0.000185
Middle Eastern	0.000109	0.000109
South Asian	0.000364	0.000359
Other	0.000164	0.000163

dbNSFP

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}.
• Pathway: Spliceosome - Homo sapiens (human);Gene expression (Transcription);RNA Polymerase II Transcription;Metabolism of RNA;Cleavage of Growing Transcript in the Termination Region ;RNA Polymerase II Transcription Termination;Transport of Mature mRNA derived from an Intron-Containing Transcript;mRNA 3,-end processing;Transport of Mature Transcript to Cytoplasm;Processing of Capped Intron-Containing Pre-mRNA (Consensus)

Recessive Scores

• pRec: 0.125

Intolerance Scores

• loftool: 0.892
• rvis_EVS: -0.09
• rvis_percentile_EVS: 46.92

Haploinsufficiency Scores

• pHI: 0.252
• hipred: Y
• hipred_score: 0.706
• ghis: 0.600

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.681

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slu7
• Phenotype: integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); immune system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); hematopoietic system phenotype

Gene ontology

• 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;mRNA export from nucleus;intracellular protein transport;mRNA 3'-end processing;cellular response to heat
• Cellular component: nucleus;nucleoplasm;spliceosomal complex;cytoplasm;cytosol;membrane;nuclear speck;small nuclear ribonucleoprotein complex;intracellular membrane-bounded organelle;catalytic step 2 spliceosome
• Molecular function: second spliceosomal transesterification activity;protein binding;zinc ion binding;pre-mRNA 3'-splice site binding