SPCS2

signal peptidase complex subunit 2

Basic information

Region (hg38): 11:74949261-74979033

Links

ENSG00000118363 ∙ NCBI:9789 ∙ OMIM:619411 ∙ HGNC:28962 ∙ Uniprot:Q15005 ∙ 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 SPCS2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SPCS2 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			6	1		7
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	6	1	0

Variants in SPCS2

This is a list of pathogenic ClinVar variants found in the SPCS2 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-74949325-A-G		not specified	Likely benign (Dec 26, 2023)
11-74949332-G-T		not specified	Uncertain significance (Sep 04, 2024)
11-74965067-A-G		not specified	Uncertain significance (Apr 19, 2024)
11-74965113-A-G		not specified	Uncertain significance (Jul 25, 2023)
11-74965842-T-C		not specified	Uncertain significance (Nov 26, 2024)
11-74965848-C-G		not specified	Uncertain significance (Dec 17, 2023)
11-74965901-G-A		not specified	Uncertain significance (Oct 08, 2024)
11-74969577-G-T		not specified	Uncertain significance (Apr 07, 2023)
11-74969617-A-G		not specified	Uncertain significance (Feb 23, 2023)
11-74976913-A-G		not specified	Uncertain significance (May 17, 2023)
11-74976925-A-G		not specified	Uncertain significance (Jan 11, 2023)
11-74976958-A-G		not specified	Uncertain significance (Nov 23, 2024)
11-74976982-C-T		not specified	Uncertain significance (Apr 17, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SPCS2	protein_coding	protein_coding	ENST00000263672	5	29785

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.929	0.0709	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.42	75	119	0.632	0.00000557	1496
Missense in Polyphen		6	31.483	0.19058		465
Synonymous	0.395	39	42.3	0.923	0.00000207	419
Loss of Function	2.69	0	8.43	0.00	3.53e-7	120

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	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
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: 0.118

Intolerance Scores

• loftool: 0.222
• rvis_EVS: 0.01
• rvis_percentile_EVS: 54.63

Haploinsufficiency Scores

• pHI: 0.588
• hipred: N
• hipred_score: 0.411
• ghis: 0.605

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.743

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Spcs2

Gene ontology

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