SMIM43

small integral membrane protein 43

Basic information

Region (hg38): 4:121758881-121765427

Links

ENSG00000164112NCBI:132332HGNC:55077Uniprot:Q4W5P6AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

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
clinvar
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)3799196
4-121761593-C-T not specified Likely benign (Jan 03, 2025)3799197
4-121761595-A-G not specified Uncertain significance (Jul 12, 2023)2597731
4-121761628-G-C not specified Uncertain significance (Oct 29, 2021)3166590
4-121761675-T-A not specified Uncertain significance (Jan 17, 2023)2456435
4-121761841-T-G not specified Uncertain significance (Nov 30, 2022)3166591
4-121761877-A-C not specified Uncertain significance (Feb 05, 2024)3166592
4-121761880-C-A not specified Uncertain significance (Jan 29, 2025)3799198

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
SMIM43protein_codingprotein_codingENST00000337677 36495
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.03640.648125357021253590.00000798
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.07356364.70.9740.00000311829
Missense in Polyphen1518.5450.80886249
Synonymous0.7241923.50.8100.00000107264
Loss of Function0.38222.670.7481.13e-737

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.000.00
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.000.00
European (Non-Finnish)0.000009210.00000880
Middle Eastern0.000.00
South Asian0.00003320.0000330
Other0.000.00

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
ghis

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Gene ontology

Biological process
Cellular component
extracellular region;integral component of membrane
Molecular function