SMCO2

single-pass membrane protein with coiled-coil domains 2

Basic information

Region (hg38): 12:27446735-27502185

Previous symbols: [ "C12orf70" ]

Links

ENSG00000165935 ∙ NCBI:341346 ∙ ∙ HGNC:34448 ∙ Uniprot:A6NFE2 ∙ 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 SMCO2 gene.

• Inborn genetic diseases (18 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SMCO2 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			14	4		18
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	14	4	0

Variants in SMCO2

This is a list of pathogenic ClinVar variants found in the SMCO2 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-27470659-A-G		not specified	Likely benign (Nov 08, 2022)
12-27470681-A-G		not specified	Uncertain significance (Jun 22, 2021)
12-27470693-A-G		not specified	Uncertain significance (Dec 30, 2023)
12-27470717-A-G		not specified	Uncertain significance (Sep 01, 2021)
12-27472786-G-A		not specified	Uncertain significance (Oct 12, 2021)
12-27475614-A-G		not specified	Uncertain significance (Jun 02, 2023)
12-27488493-A-T		not specified	Uncertain significance (Jan 04, 2024)
12-27488512-C-T		not specified	Uncertain significance (Jul 20, 2021)
12-27488523-C-G		not specified	Uncertain significance (Dec 09, 2023)
12-27488534-G-A		not specified	Uncertain significance (Aug 30, 2022)
12-27494351-C-G		not specified	Uncertain significance (May 18, 2022)
12-27495743-G-A		not specified	Likely benign (Jul 29, 2023)
12-27495746-A-G		not specified	Uncertain significance (Sep 16, 2021)
12-27495772-A-G		not specified	Likely benign (Jan 26, 2023)
12-27495843-G-A		not specified	Uncertain significance (Sep 27, 2021)
12-27495852-C-T		not specified	Likely benign (Dec 20, 2021)
12-27501945-A-G		not specified	Uncertain significance (Apr 18, 2023)
12-27501949-T-C		not specified	Uncertain significance (Feb 15, 2023)
12-27501964-C-T		not specified	Uncertain significance (Sep 30, 2022)
12-27501975-C-G		not specified	Uncertain significance (May 10, 2023)
12-27501975-C-T		not specified	Uncertain significance (Dec 16, 2023)
12-27502066-G-A		not specified	Uncertain significance (Jan 29, 2024)
12-27502075-G-A		not specified	Uncertain significance (Jun 02, 2023)
12-27502098-G-A		not specified	Uncertain significance (Mar 07, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SMCO2	protein_coding	protein_coding	ENST00000416383	8	35376

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.91e-8	0.173	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.798	127	155	0.820	0.00000760	2284
Missense in Polyphen		33	49.805	0.66259		814
Synonymous	1.61	42	57.6	0.730	0.00000296	609
Loss of Function	0.197	12	12.8	0.941	5.39e-7	198

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

Intolerance Scores

• rvis_EVS: 0.88
• rvis_percentile_EVS: 89.02

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Smco2
• Phenotype: growth/size/body region phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); normal phenotype

Gene ontology

• Cellular component: integral component of membrane