SCPEP1

protein-coding

serine carboxypeptidase 1, the group of M14 carboxypeptidases

Gene summary

Predicted to enable serine-type carboxypeptidase activity. Predicted to be involved in negative regulation of blood pressure and retinoic acid metabolic process. Predicted to act upstream of or within blood vessel diameter maintenance. Located in extracellular exosome. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_021626.3

Inheritance

—

ClinVar variants

U:78B:3

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.81

Max pathogenic AF

—

Genomic locus

chr17:56,978,129-57,006,768

External References & Databases

Ensembl (ENSG00000121064)

Transcript & Mutation Effects

hg38 • Region Span ~28.6 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to SCPEP1 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 70

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_021626.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			4 clinvar			4
missense			67 clinvar	3 clinvar		70
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			7 clinvar			7
Total	0	0	78	3	0	81

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 33 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_021626.3	RefSeq	NP_067639.1	13	MANE Select
ENST00000262288.8	Ensembl	ENSP00000262288.3	13	MANE Select
ENST00000572591.5	Ensembl	ENSP00000459807.1	6	Standard
ENST00000572710.5	Ensembl	ENSP00000461663.1	5	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

retinoic acid metabolic process
negative regulation of blood pressure
proteolysis involved in cellular protein catabolic process
positive regulation of blood vessel diameter

Molecular Function

serine-type carboxypeptidase activity

Cellular Component

cytosol
extracellular exosome

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000262288
Coding exons: 13
Length: 28664
Individuals with no LoFs: 125649
Homozygous LoFs: 0
Heterozygous LoFs: 99
Defined: 125748
p: 0.000394

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.611	222	249	0.891	0.0000128	2951
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00031	0.00031	rare
Latino/Admixed American	0.00017	0.00017	rare
Ashkenazi Jewish	0.000099	0.000099	rare
East Asian	0.0011	0.0011	notable
Finnish	0.00014	0.00014	rare
European (Non-Finnish)	0.00047	0.00047	rare
South Asian	0.00030	0.00029	rare
Other	0.00017	0.00016	rare

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0873

Gene Damage Prediction

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