SMIM5

small integral membrane protein 5

Basic information

Region (hg38): 17:75633434-75641404

Previous symbols: [ "C17orf109" ]

Links

ENSG00000204323 ∙ NCBI:643008 ∙ ∙ HGNC:40030 ∙ Uniprot:Q71RC9 ∙ 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 SMIM5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SMIM5 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	1		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	5	1	0

Variants in SMIM5

This is a list of pathogenic ClinVar variants found in the SMIM5 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-75640220-G-A		not specified	Uncertain significance (Nov 29, 2024)
17-75640233-G-A		not specified	Likely benign (Jun 17, 2022)
17-75640235-G-A		not specified	Uncertain significance (Jul 02, 2024)
17-75640297-C-G		not specified	Uncertain significance (Jun 27, 2022)
17-75640307-T-C		not specified	Uncertain significance (Nov 10, 2022)
17-75640791-C-A		not specified	Uncertain significance (Oct 09, 2024)
17-75640811-C-A		not specified	Uncertain significance (Oct 21, 2024)
17-75640836-C-T		not specified	Uncertain significance (Nov 10, 2024)
17-75640856-C-T		not specified	Uncertain significance (Aug 15, 2023)
17-75640865-A-G		not specified	Uncertain significance (Nov 17, 2022)
17-75640884-C-T		not specified	Uncertain significance (Jan 26, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SMIM5	protein_coding	protein_coding	ENST00000537494	2	7971

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.133	0.635	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.188	40	43.5	0.920	0.00000275	482
Missense in Polyphen		10	12.323	0.81151		144
Synonymous	0.540	17	20.1	0.847	0.00000133	163
Loss of Function	0.538	1	1.77	0.564	7.51e-8	23

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

Intolerance Scores

• rvis_EVS: 0.12
• rvis_percentile_EVS: 62.38

Haploinsufficiency Scores

• ghis: 0.430

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: Smim5

Gene ontology

• Cellular component: integral component of membrane