CST5

cystatin D, the group of Cystatins, type 2

Basic information

Region (hg38): 20:23875934-23879748

Links

ENSG00000170367 ∙ NCBI:1473 ∙ OMIM:123858 ∙ HGNC:2477 ∙ Uniprot:P28325 ∙ 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 CST5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CST5 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			18			18
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	18	0	0

Variants in CST5

This is a list of pathogenic ClinVar variants found in the CST5 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-23876199-G-A		not specified	Uncertain significance (Apr 12, 2022)
20-23876233-C-G		not specified	Uncertain significance (Nov 15, 2021)
20-23876241-C-A		not specified	Uncertain significance (Oct 06, 2024)
20-23876266-C-G		not specified	Uncertain significance (Aug 28, 2023)
20-23877512-A-G		not specified	Uncertain significance (Jul 06, 2021)
20-23877548-T-C		not specified	Uncertain significance (Nov 10, 2024)
20-23877563-G-A		not specified	Uncertain significance (Aug 20, 2024)
20-23877582-A-G		not specified	Uncertain significance (Aug 26, 2024)
20-23877596-T-C		not specified	Uncertain significance (Sep 03, 2024)
20-23877603-T-G		not specified	Uncertain significance (May 17, 2023)
20-23877611-C-A		not specified	Uncertain significance (May 04, 2022)
20-23877617-A-C		not specified	Uncertain significance (Jan 30, 2024)
20-23879453-T-A		not specified	Uncertain significance (Feb 11, 2022)
20-23879475-G-T		not specified	Uncertain significance (Mar 23, 2022)
20-23879505-C-T		not specified	Uncertain significance (Sep 13, 2023)
20-23879516-T-G		not specified	Uncertain significance (Dec 20, 2021)
20-23879540-C-A		not specified	Uncertain significance (May 11, 2022)
20-23879540-C-T		not specified	Uncertain significance (Sep 15, 2021)
20-23879555-T-C		not specified	Uncertain significance (Sep 08, 2024)
20-23879570-G-A		not specified	Uncertain significance (Jul 20, 2021)
20-23879576-A-G		not specified	Uncertain significance (Dec 03, 2024)
20-23879586-C-T		not specified	Uncertain significance (Feb 06, 2023)
20-23879610-C-T		not specified	Uncertain significance (Feb 23, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CST5	protein_coding	protein_coding	ENST00000304710	3	3816

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000689	0.164	125712	0	21	125733	0.0000835

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.34	113	79.3	1.42	0.00000421	934
Missense in Polyphen		26	16.918	1.5368		204
Synonymous	-1.25	42	32.9	1.28	0.00000184	265
Loss of Function	-0.606	7	5.47	1.28	2.99e-7	55

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000615	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.0000925	0.0000924
European (Non-Finnish)	0.000106	0.000106
Middle Eastern	0.0000544	0.0000544
South Asian	0.000163	0.000163
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Cysteine proteinase inhibitor that possibly plays a protective role against proteinases present in the oral cavity. The order of preference for inhibition is cathepsin S > cathepsin H > cathepsin L > cathepsin B. {ECO:0000269|PubMed:8083219}.
• Pathway: Salivary secretion - Homo sapiens (human);Endochondral Ossification (Consensus)

Recessive Scores

• pRec: 0.0862

Intolerance Scores

• loftool: 0.627
• rvis_EVS: 0.53
• rvis_percentile_EVS: 80.73

Haploinsufficiency Scores

• pHI: 0.0707
• hipred: N
• hipred_score: 0.112

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.539

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cst10
• Phenotype: limbs/digits/tail phenotype; skeleton phenotype

Gene ontology

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