SEC11A

SEC11 homolog A, signal peptidase complex subunit

Basic information

Region (hg38): 15:84669538-84716460

Previous symbols: [ "SEC11L1" ]

Links

ENSG00000140612 ∙ NCBI:23478 ∙ OMIM:618258 ∙ HGNC:17718 ∙ Uniprot:P67812 ∙ 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 SEC11A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SEC11A 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			8			8
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	8	0	0

Variants in SEC11A

This is a list of pathogenic ClinVar variants found in the SEC11A region.

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

Position	Type	Phenotype	Significance	ClinVar
15-84670040-G-C		not specified	Uncertain significance (Oct 29, 2021)
15-84670047-C-T		not specified	Uncertain significance (Mar 11, 2025)
15-84670751-G-A		not specified	Uncertain significance (Sep 27, 2024)
15-84670763-T-C		not specified	Uncertain significance (Jun 02, 2023)
15-84680735-C-G		not specified	Uncertain significance (Aug 12, 2021)
15-84680747-G-C		not specified	Uncertain significance (May 30, 2024)
15-84680788-G-A		not specified	Uncertain significance (Dec 16, 2023)
15-84691641-A-G		not specified	Uncertain significance (Jun 16, 2023)
15-84716044-C-T		not specified	Uncertain significance (Feb 14, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SEC11A	protein_coding	protein_coding	ENST00000268220	6	47173

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00225	0.929	124595	0	8	124603	0.0000321

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.58	53	96.8	0.547	0.00000496	1161
Missense in Polyphen		15	40.266	0.37252		459
Synonymous	0.439	31	34.3	0.905	0.00000183	346
Loss of Function	1.59	6	11.9	0.504	8.41e-7	118

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000692	0.0000646
Ashkenazi Jewish	0.00	0.00
East Asian	0.000114	0.000111
Finnish	0.00	0.00
European (Non-Finnish)	0.0000367	0.0000354
Middle Eastern	0.000114	0.000111
South Asian	0.00	0.00
Other	0.000208	0.000165

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Component of the microsomal signal peptidase complex which removes signal peptides from nascent proteins as they are translocated into the lumen of the endoplasmic reticulum. {ECO:0000250}.
• Pathway: Protein export - Homo sapiens (human);Synthesis, secretion, and inactivation of Glucose-dependent Insulinotropic Polypeptide (GIP);Incretin synthesis, secretion, and inactivation;Peptide hormone metabolism;SRP-dependent cotranslational protein targeting to membrane;Synthesis, secretion, and deacylation of Ghrelin;Translation;Metabolism of proteins;Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) (Consensus)

Recessive Scores

• pRec: 0.142

Intolerance Scores

• loftool: 0.437
• rvis_EVS: -0.03
• rvis_percentile_EVS: 51.04

Haploinsufficiency Scores

• pHI: 0.396
• hipred: Y
• hipred_score: 0.570
• ghis: 0.658

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.781

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Low	Low	Low
Primary Immunodeficiency	Low	Low	Low
Cancer	Low	Low	Low

Mouse Genome Informatics

• Gene name: Sec11a

Gene ontology

• Biological process: signal peptide processing
• Cellular component: signal peptidase complex;endoplasmic reticulum membrane;integral component of membrane;organelle membrane
• Molecular function: peptidase activity;serine-type peptidase activity