CST9

cystatin 9, the group of Cystatins, type 2

Basic information

Region (hg38): 20:23602410-23605917

Links

ENSG00000173335 ∙ NCBI:128822 ∙ OMIM:616543 ∙ HGNC:13261 ∙ Uniprot:Q5W186 ∙ 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 CST9 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CST9 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				1		1
missense			11	2		13
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	11	3	0

Variants in CST9

This is a list of pathogenic ClinVar variants found in the CST9 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-23603529-G-A		not specified	Likely benign (Oct 26, 2021)
20-23603533-T-A		not specified	Uncertain significance (Nov 03, 2023)
20-23603538-T-A		not specified	Uncertain significance (Jul 06, 2021)
20-23603568-C-T		not specified	Uncertain significance (Aug 05, 2024)
20-23603580-C-T		not specified	Uncertain significance (Mar 31, 2024)
20-23603587-T-C		not specified	Uncertain significance (Mar 12, 2024)
20-23603620-C-T		not specified	Uncertain significance (Jan 26, 2022)
20-23603622-T-C		not specified	Uncertain significance (Jan 25, 2023)
20-23603658-T-C		not specified	Uncertain significance (Dec 13, 2022)
20-23603686-C-T		not specified	Uncertain significance (Jun 19, 2024)
20-23603694-C-T		not specified	Uncertain significance (Jun 03, 2022)
20-23603695-G-A		not specified	Uncertain significance (Jan 03, 2024)
20-23605631-C-G		not specified	Uncertain significance (Sep 10, 2024)
20-23605672-C-T		not specified	Uncertain significance (Oct 25, 2024)
20-23605688-G-A			Likely benign (Feb 01, 2023)
20-23605729-T-C			Likely benign (Feb 01, 2023)
20-23605735-C-A		not specified	Uncertain significance (Jan 30, 2024)
20-23605828-C-A		not specified	Uncertain significance (Jan 23, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CST9	protein_coding	protein_coding	ENST00000376971	2	3467

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00109	0.397	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.206	96	90.5	1.06	0.00000500	1065
Missense in Polyphen		21	20.32	1.0335		270
Synonymous	-0.0694	37	36.5	1.01	0.00000226	293
Loss of Function	-0.288	4	3.42	1.17	1.47e-7	38

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in testis development (By similarity). May play a role in hematopoietic differentiation or inflammation (PubMed:12535658). Has immunomodulatory and antimicrobial functions against Francisella tularensis, a Gram-negative bacteria (PubMed:23922243). {ECO:0000250|UniProtKB:Q9Z0H6, ECO:0000269|PubMed:12535658, ECO:0000269|PubMed:23922243}.

Recessive Scores

• pRec: 0.106

Intolerance Scores

• loftool: 0.579
• rvis_EVS: 0.51
• rvis_percentile_EVS: 80.01

Haploinsufficiency Scores

• pHI: 0.0828
• hipred: N
• hipred_score: 0.112

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.00462

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cst9
• Phenotype: cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); normal phenotype; reproductive system phenotype

Gene ontology

• Biological process: negative regulation of endopeptidase activity;antimicrobial humoral response
• Cellular component: extracellular region
• Molecular function: cysteine-type endopeptidase inhibitor activity