SMIM20

small integral membrane protein 20, the group of Mitochondrial respiratory chain complex assembly factors

Basic information

Region (hg38): 4:25861829-25929813

Previous symbols: [ "C4orf52" ]

Links

ENSG00000250317 ∙ NCBI:389203 ∙ OMIM:617465 ∙ HGNC:37260 ∙ Uniprot:Q8N5G0 ∙ 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 SMIM20 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SMIM20 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			6			6
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	6	0	0

Variants in SMIM20

This is a list of pathogenic ClinVar variants found in the SMIM20 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-25862719-G-T		not specified	Uncertain significance (Mar 19, 2024)
4-25862775-A-G		not specified	Likely benign (Apr 07, 2023)
4-25862799-T-C		not specified	Uncertain significance (Apr 07, 2023)
4-25862805-G-T		not specified	Uncertain significance (Jun 24, 2022)
4-25862811-C-A		not specified	Uncertain significance (Jan 19, 2024)
4-25862827-G-A		not specified	Uncertain significance (Apr 07, 2023)
4-25914347-G-C		not specified	Uncertain significance (Nov 27, 2023)
4-25914371-G-T		not specified	Uncertain significance (Sep 26, 2023)
4-25914380-T-C		not specified	Uncertain significance (Nov 09, 2022)
4-25914408-G-A		not specified	Uncertain significance (Feb 27, 2024)
4-25928334-G-A		not specified	Uncertain significance (Sep 27, 2021)
4-25928336-G-T		not specified	Uncertain significance (Sep 30, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SMIM20	protein_coding	protein_coding	ENST00000506197	3	67984

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.575	0.384	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.629	21	30.8	0.681	0.00000140	421
Missense in Polyphen		14	17.997	0.77789		266
Synonymous	-0.762	16	12.6	1.27	5.53e-7	129
Loss of Function	1.50	0	2.63	0.00	1.11e-7	42

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

• Function: FUNCTION: Component of the MITRAC (mitochondrial translation regulation assembly intermediate of cytochrome c oxidase complex) complex, that regulates cytochrome c oxidase assembly. Promotes the progression of complex assembly after the association of MT- CO1/COX1 with COX4I1 and COX6C. Chaperone-like assembly factor required to stabilize newly synthesized MT-CO1/COX1 and to prevent its premature turnover. {ECO:0000269|PubMed:26321642}.

Intolerance Scores

• rvis_EVS: 0.17
• rvis_percentile_EVS: 65.04

Haploinsufficiency Scores

• ghis: 0.591

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: Smim20

Gene ontology

• Biological process: mitochondrial respiratory chain complex IV assembly
• Cellular component: mitochondrial inner membrane;integral component of membrane
• Molecular function: protein binding