SMU1

SMU1 DNA replication regulator and spliceosomal factor, the group of Spliceosomal B complex|WD repeat domain containing

Basic information

Region (hg38): 9:33041765-33076674

Links

ENSG00000122692 ∙ NCBI:55234 ∙ OMIM:617811 ∙ HGNC:18247 ∙ Uniprot:Q2TAY7 ∙ 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 SMU1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SMU1 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				1		1
missense			9			9
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	9	1	0

Variants in SMU1

This is a list of pathogenic ClinVar variants found in the SMU1 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-33048206-C-G		not specified	Uncertain significance (Nov 25, 2024)
9-33056892-T-G			Uncertain significance (Sep 03, 2021)
9-33056951-T-A		not specified	Uncertain significance (Nov 23, 2022)
9-33057638-G-C		not specified	Uncertain significance (Nov 08, 2024)
9-33060497-C-G		not specified	Uncertain significance (Nov 13, 2024)
9-33060502-A-G		not specified	Uncertain significance (Jun 28, 2024)
9-33068872-G-A			Likely benign (Jul 01, 2022)
9-33068933-G-A		not specified	Uncertain significance (Feb 27, 2024)
9-33071744-C-T		not specified	Uncertain significance (Jun 07, 2024)
9-33073612-A-G		not specified	Uncertain significance (Oct 25, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SMU1	protein_coding	protein_coding	ENST00000397149	12	34904

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.0000576	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	4.31	76	279	0.273	0.0000137	3404
Missense in Polyphen		9	59.25	0.1519		785
Synonymous	0.962	85	97.1	0.876	0.00000483	947
Loss of Function	4.87	0	27.7	0.00	0.00000139	320

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in pre-mRNA splicing as a component of the spliceosome (PubMed:28781166). Regulates alternative splicing of the HSPG2 pre-mRNA (By similarity). Required for normal accumulation of IK (PubMed:24945353). Required for normal mitotic spindle assembly and normal progress through mitosis (By similarity). {ECO:0000250|UniProtKB:Q76B40, ECO:0000269|PubMed:24945353, ECO:0000269|PubMed:28781166, ECO:0000305}.
• Pathway: EGFR1 (Consensus)

Recessive Scores

• pRec: 0.142

Intolerance Scores

• rvis_EVS: -0.14
• rvis_percentile_EVS: 42.88

Haploinsufficiency Scores

• pHI: 0.195
• hipred: Y
• hipred_score: 0.825
• ghis: 0.655

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.873

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Smu1

Gene ontology

• Biological process: regulation of alternative mRNA splicing, via spliceosome;mRNA splicing, via spliceosome;RNA splicing
• Cellular component: nucleus;cytoplasm;nuclear speck;U2-type precatalytic spliceosome
• Molecular function: protein binding