SEC61A2

SEC61 translocon subunit alpha 2

Basic information

Region (hg38): 10:12129637-12169961

Links

ENSG00000065665 ∙ NCBI:55176 ∙ OMIM:618271 ∙ HGNC:17702 ∙ Uniprot:Q9H9S3 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SEC61A2 gene.

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.

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			18			18
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1			1
Total	0	0	19	0	0

Variants in SEC61A2

This is a list of pathogenic ClinVar variants found in the SEC61A2 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-12133244-A-G		not specified	Uncertain significance (Jul 26, 2024)
10-12133280-T-C		not specified	Uncertain significance (Oct 06, 2024)
10-12133298-C-T		not specified	Uncertain significance (Oct 01, 2024)
10-12133303-A-G		not specified	Uncertain significance (Oct 30, 2023)
10-12133304-G-A		not specified	Uncertain significance (Mar 08, 2024)
10-12136142-C-T		not specified	Uncertain significance (Sep 30, 2024)
10-12149858-G-C		not specified	Uncertain significance (Dec 10, 2024)
10-12149928-G-C		not specified	Uncertain significance (Jun 12, 2023)
10-12155823-C-A		Autosomal dominant polycystic liver disease	Likely benign (Sep 01, 2021)
10-12155899-C-T		not specified	Uncertain significance (Nov 19, 2022)
10-12156930-A-G		not specified	Uncertain significance (May 14, 2024)
10-12157050-G-A		not specified	Uncertain significance (Jun 28, 2024)
10-12160939-G-A		not specified	Uncertain significance (Jun 28, 2024)
10-12160996-C-G		not specified	Uncertain significance (Dec 20, 2022)
10-12161003-C-A		not specified	Uncertain significance (Nov 10, 2024)
10-12161006-T-C		not specified	Uncertain significance (Mar 28, 2024)
10-12161038-G-A		not specified	Uncertain significance (Dec 28, 2023)
10-12161070-T-G		not specified	Uncertain significance (Dec 12, 2023)
10-12164344-A-G		not specified	Uncertain significance (May 05, 2023)
10-12167731-G-A		not specified	Uncertain significance (Oct 03, 2023)

GnomAD

Source: gnomAD

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: dbNSFP

• 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

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