CST9L

cystatin 9 like, the group of Cystatins, type 2

Basic information

Region (hg38): 20:23564732-23568484

Links

ENSG00000101435 ∙ NCBI:128821 ∙ OMIM:616536 ∙ HGNC:16233 ∙ Uniprot:Q9H4G1 ∙ 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 CST9L gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CST9L 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			10			10
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	10	0	0

Variants in CST9L

This is a list of pathogenic ClinVar variants found in the CST9L region.

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

Position	Type	Phenotype	Significance	ClinVar
20-23568224-G-T		not specified	Uncertain significance (Nov 15, 2021)
20-23568232-G-C		not specified	Uncertain significance (Oct 21, 2024)
20-23568281-G-A		not specified	Uncertain significance (Jul 19, 2023)
20-23568293-A-G		not specified	Uncertain significance (Oct 04, 2022)
20-23568308-G-A		not specified	Uncertain significance (Nov 20, 2024)
20-23568309-G-A		not specified	Uncertain significance (Jan 04, 2024)
20-23568315-A-T		not specified	Uncertain significance (Oct 10, 2023)
20-23568324-T-C		not specified	Uncertain significance (Feb 28, 2023)
20-23568341-C-T		not specified	Uncertain significance (Jul 08, 2022)
20-23568377-A-G		not specified	Uncertain significance (Oct 20, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CST9L	protein_coding	protein_coding	ENST00000376979	3	4018

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.99e-12	0.00242	125504	3	233	125740	0.000939

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.469	86	74.6	1.15	0.00000364	970
Missense in Polyphen		23	19.217	1.1968		289
Synonymous	0.0805	31	31.6	0.982	0.00000161	268
Loss of Function	-2.71	13	5.89	2.21	2.51e-7	68

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000412	0.000412
Ashkenazi Jewish	0.00268	0.00268
East Asian	0.00	0.00
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000493	0.000492
Middle Eastern	0.00	0.00
South Asian	0.00457	0.00448
Other	0.000489	0.000489

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.773
• rvis_EVS: 0.93
• rvis_percentile_EVS: 89.66

Haploinsufficiency Scores

• pHI: 0.0926
• 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: 0.0314

Gene Damage Prediction

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

Gene ontology

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