PCSK7

proprotein convertase subtilisin/kexin type 7, the group of Proprotein convertase subtilisin/kexin family

Basic information

Region (hg38): 11:117204336-117232525

Links

ENSG00000160613 ∙ NCBI:9159 ∙ OMIM:604872 ∙ HGNC:8748 ∙ Uniprot:Q16549 ∙ 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 PCSK7 gene.

• Inborn genetic diseases (20 variants)
• not provided (6 variants)
• Pericallosal lipoma;Skin tags;Preauricular skin tag (1 variants)
• Midline facial cleft;Skin tags;Pericallosal lipoma (1 variants)
• Hereditary breast ovarian cancer syndrome (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PCSK7 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				4		4
missense			23		1	24
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	23	4	1

Variants in PCSK7

This is a list of pathogenic ClinVar variants found in the PCSK7 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-117206025-G-A			Benign (Dec 31, 2019)
11-117206067-T-G		not specified	Uncertain significance (Mar 02, 2023)
11-117206071-G-C		not specified	Uncertain significance (Jul 20, 2021)
11-117206158-C-T		not specified	Uncertain significance (Nov 22, 2023)
11-117206295-T-C		not specified	Uncertain significance (May 05, 2023)
11-117206302-C-T		not specified	Uncertain significance (Nov 15, 2021)
11-117206349-A-G		not specified	Uncertain significance (Nov 14, 2023)
11-117206762-G-A			Likely benign (Aug 01, 2022)
11-117207094-C-G		not specified	Uncertain significance (Aug 17, 2022)
11-117207963-G-A			Benign (Jun 08, 2017)
11-117207986-A-C			Likely benign (Jun 08, 2017)
11-117208910-G-C		Midline facial cleft;Skin tags;Pericallosal lipoma	Uncertain significance (-)
11-117208954-T-G		Pericallosal lipoma;Skin tags;Preauricular skin tag	Uncertain significance (-)
11-117208972-C-T		not specified	Uncertain significance (Aug 15, 2023)
11-117209007-A-G			Likely benign (Feb 01, 2023)
11-117218490-G-A		not specified	Uncertain significance (Aug 17, 2022)
11-117218535-C-T		not specified	Uncertain significance (Nov 08, 2021)
11-117218538-A-G		not specified	Uncertain significance (May 11, 2022)
11-117219151-C-T		not specified	Likely benign (Mar 01, 2024)
11-117219163-T-C		not specified	Uncertain significance (Nov 17, 2023)
11-117219602-T-C		not specified	Uncertain significance (Jan 30, 2024)
11-117223213-T-C		not specified	Uncertain significance (May 23, 2023)
11-117223215-C-T		not specified	Uncertain significance (Dec 21, 2023)
11-117224087-C-T		not specified	Uncertain significance (Oct 14, 2023)
11-117224748-G-C		not specified	Uncertain significance (Jun 24, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PCSK7	protein_coding	protein_coding	ENST00000320934	15	28189

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00419	0.996	125425	0	323	125748	0.00129

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.49	373	463	0.806	0.0000282	5079
Missense in Polyphen		133	205.01	0.64874		2117
Synonymous	0.378	178	185	0.965	0.0000118	1542
Loss of Function	3.80	11	35.4	0.311	0.00000180	392

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00162	0.00160
Ashkenazi Jewish	0.0000998	0.0000992
East Asian	0.000947	0.000925
Finnish	0.000609	0.000601
European (Non-Finnish)	0.00192	0.00190
Middle Eastern	0.000947	0.000925
South Asian	0.000634	0.000621
Other	0.00183	0.00179

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Serine endoprotease that processes various proproteins by cleavage at paired basic amino acids, recognizing the RXXX[KR]R consensus motif. Likely functions in the constitutive secretory pathway.

Recessive Scores

• pRec: 0.105

Intolerance Scores

• loftool: 0.358
• rvis_EVS: -0.75
• rvis_percentile_EVS: 13.67

Haploinsufficiency Scores

• pHI: 0.429
• hipred: Y
• hipred_score: 0.520
• ghis: 0.564

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.204

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pcsk7

Zebrafish Information Network

• Gene name: pcsk7
• Affected structure: otolith
• Phenotype tag: abnormal
• Phenotype quality: decreased amount

Gene ontology

• Biological process: protein processing;peptide hormone processing
• Cellular component: trans-Golgi network;membrane;integral component of Golgi membrane
• Molecular function: serine-type endopeptidase activity;peptidase activity