SEC62
Basic information
Region (hg38): 3:169966635-169998373
Previous symbols: [ "TLOC1" ]
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the SEC62 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 | 2 | |||||
| missense | 12 | 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 | 12 | 0 | 2 |
Variants in SEC62
This is a list of pathogenic ClinVar variants found in the SEC62 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 3-169966841-C-A | not specified | Uncertain significance (Dec 13, 2022) | ||
| 3-169966855-C-G | not specified | Uncertain significance (Jul 30, 2024) | ||
| 3-169975646-C-G | Benign (Jul 23, 2018) | |||
| 3-169982737-C-G | Benign (Jul 23, 2018) | |||
| 3-169982799-C-A | not specified | Uncertain significance (Jan 21, 2025) | ||
| 3-169982802-A-G | not specified | Uncertain significance (Aug 05, 2024) | ||
| 3-169982840-A-T | not specified | Uncertain significance (Feb 24, 2025) | ||
| 3-169983170-C-T | not specified | Uncertain significance (Dec 20, 2023) | ||
| 3-169988255-C-T | not specified | Uncertain significance (Jul 09, 2024) | ||
| 3-169988276-G-C | not specified | Uncertain significance (Oct 26, 2022) | ||
| 3-169992714-A-G | not specified | Uncertain significance (Aug 19, 2024) | ||
| 3-169992762-A-G | not specified | Uncertain significance (Dec 28, 2023) | ||
| 3-169992806-A-G | not specified | Uncertain significance (Jun 23, 2021) | ||
| 3-169992870-G-A | not specified | Uncertain significance (Feb 14, 2024) | ||
| 3-169992879-G-A | not specified | Uncertain significance (Jan 02, 2024) | ||
| 3-169992902-A-G | not specified | Uncertain significance (Oct 17, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| SEC62 | protein_coding | protein_coding | ENST00000337002 | 8 | 31739 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.983 | 0.0170 | 125714 | 0 | 3 | 125717 | 0.0000119 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.78 | 130 | 201 | 0.646 | 0.00000942 | 2643 |
| Missense in Polyphen | 13 | 18.44 | 0.70498 | 251 | ||
| Synonymous | 0.0668 | 67 | 67.7 | 0.990 | 0.00000326 | 676 |
| Loss of Function | 3.87 | 2 | 21.2 | 0.0943 | 0.00000117 | 269 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000642 | 0.0000615 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000192 | 0.0000176 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Mediates post-translational transport of precursor polypeptides across endoplasmic reticulum (ER). Proposed to act as a targeting receptor for small presecretory proteins containing short and apolar signal peptides. Targets and properly positions newly synthesized presecretory proteins into the SEC61 channel- forming translocon complex, triggering channel opening for polypeptide translocation to the ER lumen. {ECO:0000269|PubMed:22375059, ECO:0000269|PubMed:29719251}.;
- Pathway
- Protein export - Homo sapiens (human);Protein processing in endoplasmic reticulum - Homo sapiens (human);miR-targeted genes in epithelium - TarBase;miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in muscle cell - TarBase;XBP1(S) activates chaperone genes;IRE1alpha activates chaperones;Unfolded Protein Response (UPR);Metabolism of proteins
(Consensus)
Recessive Scores
- pRec
- 0.122
Intolerance Scores
- loftool
- 0.200
- rvis_EVS
- 0.37
- rvis_percentile_EVS
- 75.12
Haploinsufficiency Scores
- pHI
- 0.733
- hipred
- Y
- hipred_score
- 0.783
- ghis
- 0.480
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.378
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Sec62
- Phenotype
Gene ontology
- Biological process
- cotranslational protein targeting to membrane;posttranslational protein targeting to endoplasmic reticulum membrane;posttranslational protein targeting to membrane, translocation
- Cellular component
- endoplasmic reticulum;endoplasmic reticulum membrane;rough endoplasmic reticulum;cytosol;membrane;integral component of membrane;integral component of endoplasmic reticulum membrane
- Molecular function
- protein transporter activity;signaling receptor activity