SEC61B
Basic information
Region (hg38): 9:99222064-99230615
Links
Phenotypes
GenCC
Source:
- polycystic liver disease 1 (Moderate), mode of inheritance: AD
- SEC61B-related polycystic liver disease (Limited), mode of inheritance: AD
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (7 variants)
- not_provided (2 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the SEC61B gene is commonly pathogenic or not. These statistics are base on transcript: NM_000006808.3. 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 | 7 | |||||
| nonsense | 0 | |||||
| start loss | 1 | 1 | ||||
| frameshift | 1 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 9 | 0 | 0 |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| SEC61B | protein_coding | protein_coding | ENST00000223641 | 4 | 8552 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.0200 | 0.759 | 125740 | 0 | 5 | 125745 | 0.0000199 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.03 | 35 | 56.9 | 0.615 | 0.00000318 | 592 |
| Missense in Polyphen | 8 | 18.233 | 0.43876 | 236 | ||
| Synonymous | -1.15 | 29 | 22.1 | 1.31 | 0.00000133 | 211 |
| Loss of Function | 0.849 | 3 | 5.06 | 0.593 | 2.99e-7 | 54 |
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 | 0.0000928 | 0.0000924 |
| European (Non-Finnish) | 0.0000176 | 0.0000176 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.0000327 | 0.0000327 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Component of SEC61 channel-forming translocon complex that mediates transport of signal peptide-containing precursor polypeptides across endoplasmic reticulum (ER) (By similarity). Required for PKD1/Polycystin-1 biogenesis (By similarity). {ECO:0000250|UniProtKB:P60467, ECO:0000250|UniProtKB:Q9CQS8}.;
- Disease
- DISEASE: Note=Loss-of-function SEC61B variations may cause autosomal dominant polycystic liver disease (PCLD) in patients that lack variations in known causative genes, such as PRKCSH and SEC63. {ECO:0000305|PubMed:28375157}.;
- 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
- 0.130
Intolerance Scores
- loftool
- rvis_EVS
- -0.1
- rvis_percentile_EVS
- 46.2
Haploinsufficiency Scores
- pHI
- 0.0985
- hipred
- Y
- hipred_score
- 0.800
- ghis
- 0.626
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.731
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Sec61b
- Phenotype
Gene ontology
- Biological process
- obsolete protein import into nucleus, translocation;SRP-dependent cotranslational protein targeting to membrane, translocation;ubiquitin-dependent ERAD pathway;retrograde protein transport, ER to cytosol;posttranslational protein targeting to membrane, translocation
- Cellular component
- endoplasmic reticulum;Sec61 translocon complex;endoplasmic reticulum membrane;cytosol;membrane;integral component of membrane;endoplasmic reticulum Sec complex
- Molecular function
- RNA binding;ARF guanyl-nucleotide exchange factor activity;protein binding;P-P-bond-hydrolysis-driven protein transmembrane transporter activity;epidermal growth factor binding