SCPEP1

serine carboxypeptidase 1, the group of M14 carboxypeptidases

Basic information

Region (hg38): 17:56978129-57006768

Links

ENSG00000121064 ∙ NCBI:59342 ∙ OMIM:619723 ∙ HGNC:29507 ∙ Uniprot:Q9HB40 ∙ 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 SCPEP1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SCPEP1 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			37	3		40
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	37	3	0

Variants in SCPEP1

This is a list of pathogenic ClinVar variants found in the SCPEP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-56978175-C-T		not specified	Uncertain significance (Sep 10, 2024)
17-56981091-T-C		not specified	Uncertain significance (Aug 22, 2022)
17-56981105-G-C		not specified	Uncertain significance (Feb 13, 2024)
17-56981194-G-T		not specified	Uncertain significance (Oct 01, 2024)
17-56981229-A-G		not specified	Uncertain significance (Jan 16, 2025)
17-56985385-C-T		not specified	Uncertain significance (Dec 11, 2023)
17-56985454-G-A		not specified	Uncertain significance (Oct 02, 2023)
17-56985456-A-G		not specified	Uncertain significance (Feb 21, 2024)
17-56985462-A-G		not specified	Uncertain significance (Jan 26, 2025)
17-56985463-C-G		not specified	Uncertain significance (Jul 05, 2023)
17-56987702-C-A		not specified	Uncertain significance (Apr 19, 2023)
17-56987731-G-A		not specified	Uncertain significance (Mar 08, 2025)
17-56987777-A-G		not specified	Uncertain significance (Mar 21, 2024)
17-56987785-G-T		not specified	Uncertain significance (Dec 25, 2024)
17-56987790-G-A		not specified	Uncertain significance (Mar 04, 2024)
17-56987792-T-A		not specified	Uncertain significance (Feb 27, 2024)
17-56988289-A-T		not specified	Uncertain significance (Jul 14, 2021)
17-56991100-C-T		not specified	Uncertain significance (Feb 06, 2025)
17-56991109-G-A		not specified	Likely benign (May 08, 2023)
17-56991133-C-T		not specified	Uncertain significance (Oct 22, 2021)
17-56991154-C-A		not specified	Uncertain significance (May 29, 2024)
17-56991162-T-C		not specified	Uncertain significance (Dec 16, 2023)
17-56995516-G-A		not specified	Uncertain significance (Feb 05, 2024)
17-56995604-T-A		not specified	Uncertain significance (Dec 14, 2023)
17-56995628-T-C		not specified	Uncertain significance (Dec 13, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SCPEP1	protein_coding	protein_coding	ENST00000262288	13	28664

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.23e-13	0.161	125649	0	99	125748	0.000394

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.611	222	249	0.891	0.0000128	2951
Missense in Polyphen		70	91.828	0.7623		1095
Synonymous	0.809	88	98.2	0.896	0.00000555	859
Loss of Function	0.934	23	28.4	0.811	0.00000139	312

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000481	0.000481
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.00109	0.00109
Finnish	0.000139	0.000139
European (Non-Finnish)	0.000475	0.000475
Middle Eastern	0.00109	0.00109
South Asian	0.000298	0.000294
Other	0.000166	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in vascular wall and kidney homeostasis. {ECO:0000250}.

Recessive Scores

• pRec: 0.148

Intolerance Scores

• loftool: 0.398
• rvis_EVS: -0.45
• rvis_percentile_EVS: 24.33

Haploinsufficiency Scores

• pHI: 0.158
• hipred: N
• hipred_score: 0.251
• ghis: 0.531

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0873

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Scpep1
• Phenotype: homeostasis/metabolism phenotype; normal phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan)

Gene ontology

• Biological process: retinoic acid metabolic process;negative regulation of blood pressure;proteolysis involved in cellular protein catabolic process;positive regulation of blood vessel diameter
• Cellular component: cytosol;extracellular exosome
• Molecular function: serine-type carboxypeptidase activity