SEC61B

SEC61 translocon subunit beta

Basic information

Region (hg38): 9:99222064-99230615

Links

ENSG00000106803 ∙ NCBI:10952 ∙ OMIM:609214 ∙ HGNC:16993 ∙ Uniprot:P60468 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• 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 ClinVar and linked to the SEC61B gene.

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.

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			3			3
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					4	4
Total	0	0	3	0	4

Variants in SEC61B

This is a list of pathogenic ClinVar variants found in the SEC61B region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
9-99222096-G-C			Benign (Jun 19, 2018)
9-99222364-A-G			Uncertain significance (Feb 21, 2018)
9-99222618-G-A		not specified	Uncertain significance (Mar 01, 2023)
9-99222654-C-G			Benign (May 15, 2021)
9-99227663-A-G			Benign (May 17, 2021)
9-99227771-A-G			Benign (May 17, 2021)
9-99227899-G-GAA			Uncertain significance (Feb 21, 2018)
9-99227928-C-T		not specified	Uncertain significance (Sep 01, 2021)
9-99228061-A-G			Benign (May 17, 2021)
9-99230377-G-A		not specified	Uncertain significance (Mar 01, 2024)

GnomAD

Source: gnomAD

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: dbNSFP

• 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

• 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

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