SMCO1

single-pass membrane protein with coiled-coil domains 1

Basic information

Region (hg38): 3:196506878-196515346

Previous symbols: [ "C3orf43" ]

Links

ENSG00000214097 ∙ NCBI:255798 ∙ ∙ HGNC:27407 ∙ Uniprot:Q147U7 ∙ 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 SMCO1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SMCO1 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			9	1		10
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 SMCO1

This is a list of pathogenic ClinVar variants found in the SMCO1 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-196508122-G-A		not specified	Uncertain significance (Oct 22, 2021)
3-196508173-A-G		not specified	Uncertain significance (Dec 14, 2021)
3-196508179-A-G		not specified	Uncertain significance (Aug 30, 2021)
3-196508200-C-T		not specified	Uncertain significance (Jun 22, 2024)
3-196508264-G-A		not specified	Uncertain significance (Oct 25, 2022)
3-196508266-G-A		not specified	Uncertain significance (Feb 28, 2023)
3-196508282-G-A		not specified	Uncertain significance (Oct 25, 2023)
3-196508300-T-C		not specified	Uncertain significance (Apr 17, 2023)
3-196508311-T-C		not specified	Uncertain significance (Apr 22, 2024)
3-196509529-C-T		not specified	Uncertain significance (Jan 23, 2024)
3-196509631-T-C		not specified	Likely benign (Aug 09, 2021)
3-196509643-T-G		not specified	Uncertain significance (May 11, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SMCO1	protein_coding	protein_coding	ENST00000397537	3	8490

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000155	0.449	124757	0	38	124795	0.000152

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.577	97	114	0.848	0.00000591	1400
Missense in Polyphen		20	29.192	0.68513		426
Synonymous	0.965	36	44.2	0.815	0.00000242	409
Loss of Function	0.248	6	6.69	0.897	2.79e-7	93

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000490	0.000425
Ashkenazi Jewish	0.0000994	0.0000993
East Asian	0.000390	0.000389
Finnish	0.00	0.00
European (Non-Finnish)	0.000125	0.000124
Middle Eastern	0.000390	0.000389
South Asian	0.000131	0.000131
Other	0.000165	0.000165

dbNSFP

Source: dbNSFP

Haploinsufficiency Scores

• pHI: 0.0873
• hipred: N
• hipred_score: 0.167

Essentials

• 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: Smco1

Gene ontology

• Cellular component: integral component of membrane