SMIM15

small integral membrane protein 15

Basic information

Region (hg38): 5:61157704-61162468

Previous symbols: [ "C5orf43" ]

Links

ENSG00000188725 ∙ NCBI:643155 ∙ ∙ HGNC:33861 ∙ Uniprot:Q7Z3B0 ∙ 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 SMIM15 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SMIM15 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			5			5
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	5	0	0

Variants in SMIM15

This is a list of pathogenic ClinVar variants found in the SMIM15 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-61159978-A-G		not specified	Uncertain significance (Jul 05, 2023)
5-61159990-C-T		not specified	Uncertain significance (Apr 18, 2023)
5-61160000-T-G		not specified	Uncertain significance (Jul 08, 2022)
5-61160013-C-G		not specified	Uncertain significance (Oct 03, 2024)
5-61160036-T-C		not specified	Uncertain significance (Apr 09, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SMIM15	protein_coding	protein_coding	ENST00000339020	1	4766

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.155	0.649	125726	0	14	125740	0.0000557

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.267	34	38.7	0.879	0.00000195	479
Missense in Polyphen		1	4.6327	0.21586		64
Synonymous	0.776	10	13.6	0.733	6.36e-7	138
Loss of Function	0.719	1	2.13	0.469	8.96e-8	27

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000578	0.0000578
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000791	0.0000791
Middle Eastern	0.00	0.00
South Asian	0.0000980	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• rvis_EVS: 0.52
• rvis_percentile_EVS: 80.46

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.451

Essentials

• essential_gene_CRISPR: 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: Smim15

Gene ontology

• Cellular component: integral component of membrane