OLFM4
Basic information
Region (hg38): 13:53028813-53052057
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (64 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the OLFM4 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000006418.5. Only rare variants are included in the table.
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.
Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
---|---|---|---|---|---|---|
synonymous | 1 | |||||
missense | 59 | 63 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
Total | 0 | 0 | 59 | 5 | 0 |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
OLFM4 | protein_coding | protein_coding | ENST00000219022 | 5 | 23299 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.00000278 | 0.774 | 122409 | 55 | 3284 | 125748 | 0.0134 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 0.342 | 264 | 280 | 0.942 | 0.0000150 | 3350 |
Missense in Polyphen | 79 | 92.166 | 0.85715 | 1157 | ||
Synonymous | -0.523 | 119 | 112 | 1.06 | 0.00000622 | 1009 |
Loss of Function | 1.26 | 11 | 16.5 | 0.665 | 8.53e-7 | 215 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.00831 | 0.00831 |
Ashkenazi Jewish | 0.00517 | 0.00517 |
East Asian | 0.000440 | 0.000435 |
Finnish | 0.0577 | 0.0575 |
European (Non-Finnish) | 0.0151 | 0.0150 |
Middle Eastern | 0.000440 | 0.000435 |
South Asian | 0.00161 | 0.00160 |
Other | 0.0137 | 0.0138 |
dbNSFP
Source:
- Function
- FUNCTION: May promote proliferation of pancreatic cancer cells by favoring the transition from the S to G2/M phase. In myeloid leukemic cell lines, inhibits cell growth and induces cell differentiation and apoptosis. May play a role in the inhibition of EIF4EBP1 phosphorylation/deactivation. Facilitates cell adhesion, most probably through interaction with cell surface lectins and cadherin. {ECO:0000269|PubMed:16566923, ECO:0000269|PubMed:17270022, ECO:0000269|PubMed:20724538}.;
- Pathway
- Neutrophil degranulation;Innate Immune System;Immune System
(Consensus)
Recessive Scores
- pRec
- 0.104
Intolerance Scores
- loftool
- 0.246
- rvis_EVS
- 0.53
- rvis_percentile_EVS
- 80.96
Haploinsufficiency Scores
- pHI
- 0.312
- hipred
- N
- hipred_score
- 0.146
- ghis
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.262
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Olfm4
- Phenotype
- immune system phenotype; digestive/alimentary phenotype; homeostasis/metabolism phenotype;
Gene ontology
- Biological process
- cell adhesion;regulation of necrotic cell death;regulation of apoptotic process;neutrophil degranulation;regulation of phagocytosis;protein homooligomerization;positive regulation of substrate adhesion-dependent cell spreading;regulation of neutrophil extravasation
- Cellular component
- extracellular region;extracellular space;mitochondrion;plasma membrane;secretory granule;specific granule lumen;specific granule;azurophil granule;perinuclear region of cytoplasm;extracellular exosome;tertiary granule lumen
- Molecular function
- catalytic activity;protein binding;protein homodimerization activity;cadherin binding