SMIM3

small integral membrane protein 3

Basic information

Region (hg38): 5:150778757-150796734

Previous symbols: [ "C5orf62" ]

Links

ENSG00000256235 ∙ NCBI:85027 ∙ OMIM:608324 ∙ HGNC:30248 ∙ Uniprot:Q9BZL3 ∙ 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 SMIM3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SMIM3 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			11	1		12
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	11	1	0

Variants in SMIM3

This is a list of pathogenic ClinVar variants found in the SMIM3 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-150795445-A-T		not specified	Uncertain significance (Dec 27, 2023)
5-150795496-A-G		not specified	Uncertain significance (Oct 05, 2021)
5-150795519-A-G		not specified	Uncertain significance (Jul 22, 2024)
5-150795532-T-C		not specified	Uncertain significance (Mar 20, 2023)
5-150795541-T-A		not specified	Uncertain significance (May 23, 2023)
5-150795550-T-C		not specified	Uncertain significance (Jan 23, 2024)
5-150795574-T-G		not specified	Uncertain significance (Jun 04, 2024)
5-150795583-A-G		not specified	Uncertain significance (Jun 21, 2023)
5-150795586-G-A		not specified	Uncertain significance (Jan 31, 2023)
5-150795586-G-T		not specified	Uncertain significance (Aug 22, 2023)
5-150795589-T-G		not specified	Uncertain significance (Dec 25, 2024)
5-150795610-G-A		not specified	Likely benign (Dec 14, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SMIM3	protein_coding	protein_coding	ENST00000526627	1	18789

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000138	0.136	124625	0	12	124637	0.0000481

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.802	50	36.4	1.37	0.00000199	383
Missense in Polyphen		15	12.022	1.2477		135
Synonymous	1.01	10	15.0	0.667	8.84e-7	135
Loss of Function	-3.46	4	0.755	5.29	3.25e-8	8

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000203	0.000203
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000556	0.0000556
Finnish	0.00	0.00
European (Non-Finnish)	0.0000177	0.0000177
Middle Eastern	0.0000556	0.0000556
South Asian	0.0000654	0.0000654
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.170
• ghis: 0.507

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: 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: Smim3
• Phenotype: hematopoietic system phenotype; skeleton phenotype; immune system phenotype

Gene ontology

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