SMG7

SMG7 nonsense mediated mRNA decay factor

Basic information

Region (hg38): 1:183472215-183598246

Previous symbols: [ "C1orf16" ]

Links

ENSG00000116698 ∙ NCBI:9887 ∙ OMIM:610964 ∙ HGNC:16792 ∙ Uniprot:Q92540 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• autoimmune disease (No Known Disease Relationship), mode of inheritance: AD

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SMG7 gene.

• Inborn genetic diseases (40 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SMG7 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			40			40
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	40	1	0

Variants in SMG7

This is a list of pathogenic ClinVar variants found in the SMG7 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-183515889-C-T		not specified	Uncertain significance (Mar 16, 2022)
1-183515895-A-C		not specified	Uncertain significance (Mar 29, 2023)
1-183515948-A-G		not specified	Uncertain significance (Nov 12, 2021)
1-183526684-C-T		not specified	Uncertain significance (Jan 04, 2024)
1-183529400-G-A		not specified	Uncertain significance (May 03, 2023)
1-183529494-G-T		not specified	Uncertain significance (Jun 02, 2023)
1-183529523-A-G		not specified	Uncertain significance (Apr 26, 2023)
1-183533253-T-G		not specified	Uncertain significance (Jul 21, 2021)
1-183533258-A-G		not specified	Uncertain significance (Jun 24, 2022)
1-183533677-G-A		not specified	Uncertain significance (May 27, 2022)
1-183533703-G-A		not specified	Uncertain significance (Mar 20, 2023)
1-183533736-A-G		not specified	Uncertain significance (May 05, 2023)
1-183533792-C-T		not specified	Uncertain significance (Dec 12, 2023)
1-183541001-A-G		not specified	Uncertain significance (Feb 28, 2023)
1-183541021-G-C		not specified	Uncertain significance (Dec 11, 2023)
1-183542213-A-G		not specified	Uncertain significance (Nov 30, 2021)
1-183542215-G-C		not specified	Uncertain significance (Jan 03, 2022)
1-183542216-G-A		not specified	Uncertain significance (Jul 09, 2021)
1-183542216-G-T		not specified	Uncertain significance (May 23, 2023)
1-183542267-A-G		not specified	Likely benign (Jan 19, 2024)
1-183542321-G-A		not specified	Uncertain significance (Apr 07, 2022)
1-183542326-G-C		not specified	Uncertain significance (Mar 04, 2024)
1-183544435-G-C		not specified	Uncertain significance (May 17, 2023)
1-183544489-G-C		not specified	Uncertain significance (Dec 28, 2022)
1-183545018-A-G			Likely benign (Jan 01, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SMG7	protein_coding	protein_coding	ENST00000507469	23	126031

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.0000199	125720	0	19	125739	0.0000756

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.19	466	620	0.752	0.0000314	7684
Missense in Polyphen		122	235.28	0.51852		2977
Synonymous	0.531	224	234	0.956	0.0000123	2306
Loss of Function	6.60	8	65.8	0.122	0.00000367	700

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000108	0.000102
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000744	0.0000544
Finnish	0.000200	0.000185
European (Non-Finnish)	0.000102	0.0000967
Middle Eastern	0.0000744	0.0000544
South Asian	0.00	0.00
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays a role in nonsense-mediated mRNA decay. Recruits UPF1 to cytoplasmic mRNA decay bodies. Together with SMG5 is thought to provide a link to the mRNA degradation machinery involving exonucleolytic pathways, and to serve as an adapter for UPF1 to protein phosphatase 2A (PP2A), thereby triggering UPF1 dephosphorylation. {ECO:0000269|PubMed:15546618, ECO:0000269|PubMed:15721257}.
• Pathway: mRNA surveillance pathway - Homo sapiens (human) (Consensus)

Recessive Scores

• pRec: 0.114

Intolerance Scores

• loftool: 0.413
• rvis_EVS: -0.31
• rvis_percentile_EVS: 32.23

Haploinsufficiency Scores

• pHI: 0.162
• hipred: Y
• hipred_score: 0.699
• ghis: 0.560

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.885

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Smg7

Zebrafish Information Network

• Gene name: smg7
• Affected structure: post-vent region
• Phenotype tag: abnormal
• Phenotype quality: bent

Gene ontology

• Biological process: nuclear-transcribed mRNA catabolic process, nonsense-mediated decay;mRNA export from nucleus;telomere maintenance via telomerase;regulation of telomere maintenance via telomerase;regulation of dephosphorylation;RNA phosphodiester bond hydrolysis
• Cellular component: nucleus;telomerase holoenzyme complex;cytoplasm;cytosol;intermediate filament cytoskeleton
• Molecular function: protein binding;telomeric DNA binding;protein phosphatase 2A binding;telomerase RNA binding