SMIM21

small integral membrane protein 21

Basic information

Region (hg38): 18:75409476-75427703

Previous symbols: [ "C18orf62" ]

Links

ENSG00000206026 ∙ NCBI:284274 ∙ ∙ HGNC:27598 ∙ Uniprot:Q3B7S5 ∙ 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 SMIM21 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SMIM21 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			9
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	0	0

Variants in SMIM21

This is a list of pathogenic ClinVar variants found in the SMIM21 region.

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

Position	Type	Phenotype	Significance	ClinVar
18-75410877-G-T		not specified	Uncertain significance (Sep 11, 2024)
18-75418789-C-T		not specified	Uncertain significance (Nov 22, 2024)
18-75418797-G-T		not specified	Uncertain significance (Jun 11, 2021)
18-75418817-C-A		not specified	Uncertain significance (Aug 23, 2021)
18-75418841-T-A		not specified	Uncertain significance (Mar 20, 2024)
18-75418878-C-A		not specified	Uncertain significance (Feb 27, 2023)
18-75418883-A-T		not specified	Uncertain significance (May 24, 2023)
18-75427512-C-T		not specified	Uncertain significance (May 25, 2022)
18-75427532-C-T		not specified	Uncertain significance (Mar 20, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SMIM21	protein_coding	protein_coding	ENST00000579022	3	18228

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000212	0.165	123546	0	6	123552	0.0000243

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.113	59	56.6	1.04	0.00000310	663
Missense in Polyphen		3	2.2526	1.3318		26
Synonymous	-0.770	23	18.8	1.23	8.07e-7	194
Loss of Function	-0.898	6	4.05	1.48	2.57e-7	42

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000180	0.000180
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	0.000166	0.000166

dbNSFP

Source: dbNSFP

Intolerance Scores

• rvis_EVS: 0.17
• rvis_percentile_EVS: 65.33

Haploinsufficiency Scores

• pHI: 0.0440
• hipred: N
• hipred_score: 0.123
• ghis: 0.403

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

Gene ontology

• Cellular component: integral component of membrane