SEC61A2
Basic information
Region (hg38): 10:12129637-12169961
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (24 variants)
- Autosomal_dominant_polycystic_liver_disease (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the SEC61A2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000018144.4. 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 | 0 | |||||
| missense | 24 | 25 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 24 | 1 | 0 |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| SEC61A2 | protein_coding | protein_coding | ENST00000298428 | 12 | 40325 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.00737 | 0.993 | 125727 | 0 | 21 | 125748 | 0.0000835 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 3.00 | 131 | 270 | 0.486 | 0.0000141 | 3079 |
| Missense in Polyphen | 21 | 80.559 | 0.26068 | 906 | ||
| Synonymous | 1.38 | 85 | 103 | 0.827 | 0.00000585 | 967 |
| Loss of Function | 3.34 | 9 | 28.1 | 0.320 | 0.00000171 | 304 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000178 | 0.000177 |
| Ashkenazi Jewish | 0.0000992 | 0.0000992 |
| East Asian | 0.000109 | 0.000109 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000530 | 0.0000527 |
| Middle Eastern | 0.000109 | 0.000109 |
| South Asian | 0.000133 | 0.000131 |
| Other | 0.000497 | 0.000489 |
dbNSFP
Source:
- Function
- FUNCTION: Appears to play a crucial role in the insertion of secretory and membrane polypeptides into the ER. It is required for assembly of membrane and secretory proteins. Found to be tightly associated with membrane-bound ribosomes, either directly or through adaptor proteins (By similarity). {ECO:0000250}.;
- Pathway
- Protein export - Homo sapiens (human);Phagosome - Homo sapiens (human);Protein processing in endoplasmic reticulum - Homo sapiens (human);Vibrio cholerae infection - Homo sapiens (human);XBP1(S) activates chaperone genes;SRP-dependent cotranslational protein targeting to membrane;IRE1alpha activates chaperones;Unfolded Protein Response (UPR);Translation;Metabolism of proteins;Immune System;Adaptive Immune System;Antigen processing-Cross presentation;Class I MHC mediated antigen processing & presentation;ER-Phagosome pathway
(Consensus)
Recessive Scores
- pRec
- 0.156
Intolerance Scores
- loftool
- 0.192
- rvis_EVS
- -0.43
- rvis_percentile_EVS
- 25.15
Haploinsufficiency Scores
- pHI
- 0.877
- hipred
- Y
- hipred_score
- 0.662
- ghis
- 0.639
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.544
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Sec61a2
- Phenotype
Gene ontology
- Biological process
- SRP-dependent cotranslational protein targeting to membrane, translocation;posttranslational protein targeting to endoplasmic reticulum membrane;biological_process
- Cellular component
- endoplasmic reticulum;Sec61 translocon complex;endoplasmic reticulum membrane;cytosol;integral component of membrane
- Molecular function
- molecular_function;signal sequence binding;protein transmembrane transporter activity;ribosome binding