SMUG1

single-strand-selective monofunctional uracil-DNA glycosylase 1, the group of DNA glycosylases

Basic information

Region (hg38): 12:54121277-54189008

Links

ENSG00000123415 ∙ NCBI:23583 ∙ OMIM:607753 ∙ HGNC:17148 ∙ Uniprot:Q53HV7 ∙ 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 SMUG1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SMUG1 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			15	1	1	17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	15	1	1

Variants in SMUG1

This is a list of pathogenic ClinVar variants found in the SMUG1 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-54182121-C-A		not specified	Uncertain significance (May 20, 2024)
12-54182179-T-C		not specified	Uncertain significance (Dec 05, 2022)
12-54182204-T-G		not specified	Uncertain significance (Jan 23, 2024)
12-54182262-A-G		not specified	Uncertain significance (Jul 12, 2023)
12-54182271-A-G		not specified	Uncertain significance (Dec 12, 2022)
12-54182286-C-T		not specified	Uncertain significance (May 26, 2022)
12-54182383-T-C		not specified	Uncertain significance (Jan 30, 2024)
12-54182452-C-T		not specified	Uncertain significance (May 06, 2024)
12-54182494-C-A		not specified	Uncertain significance (Apr 28, 2022)
12-54182549-C-G		not specified	Uncertain significance (Jun 22, 2021)
12-54183651-T-A		Malignant tumor of prostate	Uncertain significance (-)
12-54183685-G-C		not specified	Uncertain significance (Aug 02, 2021)
12-54183726-T-C		not specified	Uncertain significance (Dec 19, 2023)
12-54183729-C-T		not specified	Uncertain significance (Jul 20, 2021)
12-54183745-G-A		not specified	Uncertain significance (May 13, 2022)
12-54183798-G-A		not specified	Uncertain significance (May 18, 2022)
12-54183836-C-A		not specified	Uncertain significance (Feb 10, 2022)
12-54183897-C-A			Benign (Jul 06, 2018)
12-54183916-A-G		not specified	Likely benign (Sep 12, 2023)
12-54183918-C-T		not specified	Uncertain significance (Apr 05, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SMUG1	protein_coding	protein_coding	ENST00000508394	2	24250

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000452	0.877	125706	0	42	125748	0.000167

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.860	128	158	0.808	0.00000927	1708
Missense in Polyphen		51	64.493	0.79078		745
Synonymous	0.862	55	63.8	0.863	0.00000312	607
Loss of Function	1.37	7	12.2	0.575	9.75e-7	86

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000479	0.000477
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.000139	0.000139
European (Non-Finnish)	0.000151	0.000149
Middle Eastern	0.0000544	0.0000544
South Asian	0.000263	0.000261
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Recognizes base lesions in the genome and initiates base excision DNA repair. Acts as a monofunctional DNA glycosylase specific for uracil (U) residues in DNA with a preference for single-stranded DNA substrates. The activity is greater toward mismatches (U/G) compared to matches (U/A). Excises uracil (U), 5- formyluracil (fU) and uracil derivatives bearing an oxidized group at C5 [5-hydroxyuracil (hoU) and 5-hydroxymethyluracil (hmU)] in ssDNA and dsDNA, but not analogous cytosine derivatives (5- hydroxycytosine and 5-formylcytosine), nor other oxidized bases. The activity is damage-specific and salt-dependent. The substrate preference is the following: ssDNA > dsDNA (G pair) = dsDNA (A pair) at low salt concentration, and dsDNA (G pair) > dsDNA (A pair) > ssDNA at high salt concentration. {ECO:0000269|PubMed:10074426, ECO:0000269|PubMed:11526119, ECO:0000269|PubMed:12161446, ECO:0000269|PubMed:12718543}.
• Pathway: Fluoropyrimidine Pathway, Pharmacodynamics;Base excision repair - Homo sapiens (human);Fluoropyrimidine Activity;DNA Repair;Recognition and association of DNA glycosylase with site containing an affected pyrimidine;Cleavage of the damaged pyrimidine ;Depyrimidination;Base-Excision Repair, AP Site Formation;Resolution of Abasic Sites (AP sites);Base Excision Repair;Displacement of DNA glycosylase by APEX1 (Consensus)

Recessive Scores

• pRec: 0.174

Intolerance Scores

• loftool: 0.790
• rvis_EVS: 0.08
• rvis_percentile_EVS: 60.09

Haploinsufficiency Scores

• pHI: 0.0695
• hipred: N
• hipred_score: 0.208
• ghis: 0.514

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.992

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Smug1
• 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); neoplasm; homeostasis/metabolism phenotype; cellular phenotype

Gene ontology

• Biological process: base-excision repair;depyrimidination
• Cellular component: nucleoplasm;nucleolus
• Molecular function: oxidized pyrimidine nucleobase lesion DNA N-glycosylase activity;DNA binding;uracil DNA N-glycosylase activity;protein binding;single-strand selective uracil DNA N-glycosylase activity;DNA N-glycosylase activity