SPCS1

signal peptidase complex subunit 1

Basic information

Region (hg38): 3:52704954-52711148

Links

ENSG00000114902 ∙ NCBI:28972 ∙ OMIM:610358 ∙ HGNC:23401 ∙ Uniprot:Q9Y6A9 ∙ 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 SPCS1 gene.

• Inborn genetic diseases (5 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SPCS1 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			4	1		5
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	4	1	0

Variants in SPCS1

This is a list of pathogenic ClinVar variants found in the SPCS1 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-52706092-C-A		not specified	Uncertain significance (Dec 28, 2023)
3-52706124-G-A		not specified	Uncertain significance (Sep 07, 2022)
3-52706151-C-G		not specified	Uncertain significance (Jan 04, 2024)
3-52706165-A-C		not specified	Uncertain significance (Feb 14, 2024)
3-52706173-C-A		not specified	Uncertain significance (Jan 23, 2024)
3-52706179-T-C		not specified	Likely benign (Aug 08, 2023)
3-52706224-G-A		not specified	Uncertain significance (Nov 08, 2022)
3-52706859-G-A		not specified	Uncertain significance (Feb 16, 2023)
3-52707747-G-A		not specified	Uncertain significance (Oct 13, 2023)
3-52707754-G-A		not specified	Uncertain significance (Aug 14, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SPCS1	protein_coding	protein_coding	ENST00000233025	4	3212

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0139	0.878	125743	0	5	125748	0.0000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.462	85	97.9	0.869	0.00000476	1054
Missense in Polyphen		17	26.537	0.64061		317
Synonymous	0.466	37	40.8	0.907	0.00000205	348
Loss of Function	1.34	4	8.11	0.493	3.45e-7	91

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000352	0.0000352
Middle Eastern	0.0000544	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);Biotin Metabolism;Multiple carboxylase deficiency, neonatal or early onset form;Biotinidase Deficiency;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: 0.116

Intolerance Scores

• loftool: 0.495
• rvis_EVS: 0.3
• rvis_percentile_EVS: 71.81

Haploinsufficiency Scores

• pHI: 0.189
• hipred: Y
• hipred_score: 0.581
• ghis: 0.437

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.952

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Spcs1

Gene ontology

• Biological process: signal peptide processing;proteolysis;protein targeting to ER
• Cellular component: signal peptidase complex;endoplasmic reticulum membrane;integral component of endoplasmic reticulum membrane;organelle membrane
• Molecular function: molecular_function;protein binding;peptidase activity