SMIM43

small integral membrane protein 43

Basic information

Region (hg38): 4:121758881-121765427

Links

ENSG00000164112 ∙ NCBI:132332 ∙ ∙ HGNC:55077 ∙ Uniprot:Q4W5P6 ∙ 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 SMIM43 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SMIM43 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						0
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			5			5
Total	0	0	5	0	0

Variants in SMIM43

This is a list of pathogenic ClinVar variants found in the SMIM43 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-121761589-C-T		not specified	Uncertain significance (Feb 25, 2025)
4-121761593-C-T		not specified	Likely benign (Jan 03, 2025)
4-121761595-A-G		not specified	Uncertain significance (Jul 12, 2023)
4-121761628-G-C		not specified	Uncertain significance (Oct 29, 2021)
4-121761675-T-A		not specified	Uncertain significance (Jan 17, 2023)
4-121761841-T-G		not specified	Uncertain significance (Nov 30, 2022)
4-121761877-A-C		not specified	Uncertain significance (Feb 05, 2024)
4-121761880-C-A		not specified	Uncertain significance (Jan 29, 2025)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SMIM43	protein_coding	protein_coding	ENST00000337677	3	6495

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0364	0.648	125357	0	2	125359	0.00000798

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0735	63	64.7	0.974	0.00000311	829
Missense in Polyphen		15	18.545	0.80886		249
Synonymous	0.724	19	23.5	0.810	0.00000107	264
Loss of Function	0.382	2	2.67	0.748	1.13e-7	37

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)	0.00000921	0.00000880
Middle Eastern	0.00	0.00
South Asian	0.0000332	0.0000330
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.760
• rvis_EVS: 0.86
• rvis_percentile_EVS: 88.56

Haploinsufficiency Scores

• pHI: 1.65
• hipred: N
• hipred_score: 0.123

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0420

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Gene ontology

• Cellular component: extracellular region;integral component of membrane