CST7

cystatin F, the group of Cystatins, type 2

Basic information

Region (hg38): 20:24949269-24959928

Links

ENSG00000077984 ∙ NCBI:8530 ∙ OMIM:603253 ∙ HGNC:2479 ∙ Uniprot:O76096 ∙ 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 CST7 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CST7 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 CST7

This is a list of pathogenic ClinVar variants found in the CST7 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-24957403-T-C		not specified	Uncertain significance (Aug 21, 2023)
20-24957424-T-G		not specified	Uncertain significance (Feb 22, 2023)
20-24958972-A-C		not specified	Uncertain significance (Jan 30, 2024)
20-24958980-G-C		not specified	Uncertain significance (Aug 17, 2022)
20-24959000-C-A		not specified	Likely benign (Dec 12, 2023)
20-24959665-G-A		not specified	Uncertain significance (Mar 28, 2022)
20-24959666-T-G		not specified	Uncertain significance (May 15, 2024)
20-24959686-G-A		not specified	Uncertain significance (Mar 01, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CST7	protein_coding	protein_coding	ENST00000480798	4	10699

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.22e-7	0.0593	125654	0	92	125746	0.000366

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.603	100	84.4	1.18	0.00000472	946
Missense in Polyphen		35	24.622	1.4215		317
Synonymous	-0.0879	33	32.4	1.02	0.00000178	284
Loss of Function	-1.03	9	6.22	1.45	3.45e-7	73

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00111	0.00111
Ashkenazi Jewish	0.0000999	0.0000992
East Asian	0.000707	0.000707
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000230	0.000229
Middle Eastern	0.000707	0.000707
South Asian	0.000360	0.000359
Other	0.000654	0.000652

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Inhibits papain and cathepsin L but with affinities lower than other cystatins. May play a role in immune regulation through inhibition of a unique target in the hematopoietic system.

Recessive Scores

• pRec: 0.215

Intolerance Scores

• loftool: 0.803
• rvis_EVS: -0.01
• rvis_percentile_EVS: 53.19

Haploinsufficiency Scores

• pHI: 0.0974
• hipred: N
• hipred_score: 0.180
• ghis: 0.529

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0476

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cst7
• Phenotype: normal phenotype

Gene ontology

• Biological process: immune response;negative regulation of endopeptidase activity
• Cellular component: extracellular region;cytoplasm
• Molecular function: endopeptidase inhibitor activity;cysteine-type endopeptidase inhibitor activity;protein binding