CST2

cystatin SA, the group of Cystatins, type 2

Basic information

Region (hg38): 20:23823769-23826729

Links

ENSG00000170369 ∙ NCBI:1470 ∙ OMIM:123856 ∙ HGNC:2474 ∙ Uniprot:P09228 ∙ 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 CST2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CST2 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			27	3	1	31
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	27	3	1

Variants in CST2

This is a list of pathogenic ClinVar variants found in the CST2 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-23824054-A-C		not specified	Uncertain significance (Jul 13, 2021)
20-23824058-T-C		not specified	Uncertain significance (Jun 13, 2024)
20-23824061-C-T		not specified	Uncertain significance (Jun 07, 2024)
20-23824076-C-T		not specified	Uncertain significance (Jun 01, 2023)
20-23824085-G-C		not specified	Uncertain significance (Sep 01, 2021)
20-23824094-A-T		not specified	Uncertain significance (Jun 19, 2024)
20-23825214-T-C		not specified	Uncertain significance (Oct 20, 2021)
20-23825226-T-G		not specified	Uncertain significance (Jun 23, 2023)
20-23825235-A-G		not specified	Uncertain significance (Oct 13, 2023)
20-23825271-C-T		not specified	Uncertain significance (Aug 11, 2024)
20-23825274-A-G		not specified	Likely benign (Aug 14, 2024)
20-23825296-C-T		not specified	Uncertain significance (Oct 02, 2023)
20-23825304-T-G		not specified	Uncertain significance (Dec 15, 2023)
20-23825320-C-T		not specified	Uncertain significance (Aug 28, 2023)
20-23825322-A-G		not specified	Likely benign (Oct 20, 2024)
20-23825326-A-G			Likely benign (Feb 09, 2018)
20-23826446-C-T		not specified	Uncertain significance (Aug 04, 2024)
20-23826456-G-A			Benign (Feb 09, 2018)
20-23826478-A-T		not specified	Uncertain significance (Dec 12, 2023)
20-23826488-G-A		not specified	Uncertain significance (May 25, 2022)
20-23826491-T-C		not specified	Uncertain significance (Jun 10, 2024)
20-23826501-C-T		not specified	Uncertain significance (May 30, 2023)
20-23826512-A-C		not specified	Uncertain significance (Mar 08, 2025)
20-23826524-C-T		not specified	Uncertain significance (Jun 13, 2024)
20-23826528-G-T		not specified	Uncertain significance (Jun 05, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CST2	protein_coding	protein_coding	ENST00000304725	3	2963

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
8.06e-8	0.0467	125028	8	712	125748	0.00287

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-2.12	135	81.2	1.66	0.00000455	903
Missense in Polyphen		35	19.964	1.7531		231
Synonymous	-3.53	60	33.9	1.77	0.00000184	275
Loss of Function	-1.25	9	5.76	1.56	3.44e-7	56

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0384	0.0382
Ashkenazi Jewish	0.00	0.00
East Asian	0.000599	0.000598
Finnish	0.00	0.00
European (Non-Finnish)	0.000158	0.000158
Middle Eastern	0.000599	0.000598
South Asian	0.00140	0.00141
Other	0.000815	0.000815

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Thiol protease inhibitor.
• Pathway: Salivary secretion - Homo sapiens (human) (Consensus)

Recessive Scores

• pRec: 0.0958

Intolerance Scores

• loftool: 0.867
• rvis_EVS: 0.97
• rvis_percentile_EVS: 90.34

Haploinsufficiency Scores

• pHI: 0.0806
• hipred: N
• hipred_score: 0.112

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.175

Gene Damage Prediction

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

Gene ontology

• Biological process: detection of chemical stimulus involved in sensory perception of bitter taste;negative regulation of endopeptidase activity
• Cellular component: extracellular space
• Molecular function: cysteine-type endopeptidase inhibitor activity;protein binding