SMCO3

single-pass membrane protein with coiled-coil domains 3

Basic information

Region (hg38): 12:14804650-14814182

Previous symbols: [ "C12orf69" ]

Links

ENSG00000179256 ∙ NCBI:440087 ∙ ∙ HGNC:34401 ∙ Uniprot:A2RU48 ∙ 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 SMCO3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SMCO3 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			19			19
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	19	0	0

Variants in SMCO3

This is a list of pathogenic ClinVar variants found in the SMCO3 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-14806023-C-G		not specified	Uncertain significance (Jan 05, 2022)
12-14806026-T-C		not specified	Uncertain significance (Dec 27, 2023)
12-14806073-T-C		not specified	Uncertain significance (Oct 10, 2023)
12-14806073-T-G		not specified	Uncertain significance (May 26, 2024)
12-14806090-C-A		not specified	Uncertain significance (Apr 14, 2022)
12-14806118-A-G		not specified	Uncertain significance (Dec 20, 2023)
12-14806148-G-A		not specified	Uncertain significance (Feb 12, 2024)
12-14806152-G-A		not specified	Uncertain significance (Jun 06, 2023)
12-14806176-C-G		not specified	Uncertain significance (Dec 16, 2022)
12-14806259-G-T		not specified	Uncertain significance (Oct 04, 2022)
12-14806298-G-C		not specified	Uncertain significance (Oct 14, 2021)
12-14806311-C-T		not specified	Uncertain significance (Dec 14, 2023)
12-14806330-A-C		not specified	Uncertain significance (Apr 27, 2022)
12-14806346-A-T		not specified	Uncertain significance (Jun 18, 2021)
12-14806438-C-G		not specified	Uncertain significance (Mar 20, 2023)
12-14806475-A-G		not specified	Uncertain significance (Aug 12, 2021)
12-14806581-C-T		not specified	Uncertain significance (Aug 02, 2022)
12-14806619-A-G		not specified	Uncertain significance (Nov 07, 2022)
12-14806656-G-A		not specified	Uncertain significance (Sep 26, 2023)
12-14806671-T-C		not specified	Uncertain significance (Jul 11, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SMCO3	protein_coding	protein_coding	ENST00000316048	1	9533

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0144	0.696	124787	0	6	124793	0.0000240

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.165	125	120	1.04	0.00000582	1477
Missense in Polyphen		38	43.702	0.86952		550
Synonymous	0.504	40	44.3	0.904	0.00000213	452
Loss of Function	0.620	3	4.40	0.681	1.83e-7	68

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000869	0.0000869
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000619	0.0000556
Finnish	0.00	0.00
European (Non-Finnish)	0.00000883	0.00000883
Middle Eastern	0.0000619	0.0000556
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• rvis_EVS: 0.95
• rvis_percentile_EVS: 89.96

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.187
• ghis: 0.505

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: Smco3

Gene ontology

• Cellular component: integral component of membrane
• Molecular function: protein binding