SEC11C

SEC11 homolog C, signal peptidase complex subunit

Basic information

Region (hg38): 18:59139475-59158832

Previous symbols: [ "SEC11L3" ]

Links

ENSG00000166562 ∙ NCBI:90701 ∙ ∙ HGNC:23400 ∙ Uniprot:Q9BY50 ∙ 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 SEC11C gene.

• not_specified (9 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SEC11C gene is commonly pathogenic or not. These statistics are base on transcript: NM_000033280.4. 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	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			8	1		9
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	8	1	0

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SEC11C	protein_coding	protein_coding	ENST00000587834	6	19360

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.724	0.273	125744	0	3	125747	0.0000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.00	49	107	0.456	0.00000560	1252
Missense in Polyphen		8	24.952	0.32061		291
Synonymous	0.207	38	39.7	0.958	0.00000217	363
Loss of Function	2.40	1	8.57	0.117	3.59e-7	119

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000591	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000177	0.0000176
Middle Eastern	0.0000591	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

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: 0.107

Intolerance Scores

• loftool: 0.302
• rvis_EVS: -0.03
• rvis_percentile_EVS: 51.04

Haploinsufficiency Scores

• pHI: 0.322
• hipred: Y
• hipred_score: 0.833
• ghis: 0.600

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.567

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Sec11c

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