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.

• not_specified (42 variants)
• not_provided (2 variants)

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. These statistics are base on transcript: NM_000001322.3. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			38	4	1	43
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	38	4	1

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