CST11

cystatin 11, the group of Cystatins, type 2

Basic information

Region (hg38): 20:23450403-23452876

Previous symbols: [ "CST8L" ]

Links

ENSG00000125831 ∙ NCBI:140880 ∙ OMIM:609731 ∙ HGNC:15959 ∙ Uniprot:Q9H112 ∙ 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 CST11 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CST11 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			14	1		15
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	14	1	0

Variants in CST11

This is a list of pathogenic ClinVar variants found in the CST11 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-23450511-C-A		not specified	Uncertain significance (Jan 18, 2023)
20-23450550-A-G		not specified	Uncertain significance (Aug 12, 2024)
20-23451820-T-A		not specified	Uncertain significance (Aug 27, 2024)
20-23451821-G-A		not specified	Likely benign (Jan 09, 2025)
20-23451871-G-T		not specified	Uncertain significance (Nov 30, 2022)
20-23451872-T-C		not specified	Uncertain significance (Aug 15, 2023)
20-23451878-A-G		not specified	Likely benign (Dec 12, 2024)
20-23452588-C-T		not specified	Likely benign (Apr 19, 2024)
20-23452594-A-G		not specified	Uncertain significance (Oct 25, 2024)
20-23452606-C-T		not specified	Uncertain significance (Dec 31, 2024)
20-23452613-T-A		not specified	Uncertain significance (May 03, 2023)
20-23452614-C-A		not specified	Uncertain significance (May 03, 2023)
20-23452655-C-T		not specified	Uncertain significance (Jan 18, 2023)
20-23452702-A-G		not specified	Uncertain significance (Nov 17, 2023)
20-23452712-C-T		not specified	Uncertain significance (Oct 21, 2021)
20-23452739-G-T		not specified	Uncertain significance (Apr 12, 2022)
20-23452751-C-G		not specified	Uncertain significance (Jan 30, 2024)
20-23452804-G-C		not specified	Uncertain significance (Oct 12, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CST11	protein_coding	protein_coding	ENST00000377009	3	2455

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000788	0.327	125468	0	277	125745	0.00110

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.391	80	70.7	1.13	0.00000341	928
Missense in Polyphen		11	19.578	0.56185		268
Synonymous	-0.380	30	27.5	1.09	0.00000143	230
Loss of Function	-0.105	6	5.73	1.05	2.45e-7	62

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000207	0.000207
Ashkenazi Jewish	0.00	0.00
East Asian	0.0134	0.0135
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000132	0.000123
Middle Eastern	0.0134	0.0135
South Asian	0.000196	0.000196
Other	0.000489	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Has antibacterial activity against the Gram-negative bacteria E.coli. May play a role in sperm maturation and fertilization. {ECO:0000269|PubMed:12072414}.

Recessive Scores

• pRec: 0.0678

Intolerance Scores

• loftool: 0.820
• rvis_EVS: -0.07
• rvis_percentile_EVS: 48.12

Haploinsufficiency Scores

• pHI: 0.0173
• hipred: N
• hipred_score: 0.123
• ghis: 0.441

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0602

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cst11

Gene ontology

• Biological process: negative regulation of endopeptidase activity;androgen receptor signaling pathway;killing of cells of other organism;defense response to Gram-negative bacterium
• Cellular component: extracellular region;nucleus;cytoplasm;sperm flagellum;sperm head
• Molecular function: cysteine-type endopeptidase inhibitor activity