CSTL1

cystatin like 1, the group of Cystatins, type 2

Basic information

Region (hg38): 20:23426104-23444930

Links

ENSG00000125823NCBI:128817HGNC:15958Uniprot:Q9H114AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CSTL1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CSTL1 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
15
clinvar
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 15 0 0

Variants in CSTL1

This is a list of pathogenic ClinVar variants found in the CSTL1 region.

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

Position Type Phenotype Significance ClinVar
20-23440291-C-A not specified Uncertain significance (Feb 17, 2023)2473838
20-23440337-C-T not specified Uncertain significance (Jul 25, 2024)3498010
20-23440373-A-T not specified Uncertain significance (May 14, 2024)3269977
20-23440404-A-T not specified Uncertain significance (Jan 10, 2022)2271538
20-23440411-C-A not specified Uncertain significance (Oct 12, 2024)3498011
20-23440419-C-A not specified Uncertain significance (Jul 20, 2021)2222407
20-23440435-C-A not specified Uncertain significance (Sep 08, 2024)2226435
20-23440440-A-T not specified Uncertain significance (Aug 02, 2021)2240232
20-23440475-A-G not specified Uncertain significance (Dec 31, 2023)3078466
20-23443938-C-T not specified Uncertain significance (Nov 21, 2024)3498009
20-23443941-C-T not specified Uncertain significance (Jul 19, 2023)2600070
20-23443971-T-C not specified Uncertain significance (Mar 16, 2022)2350247
20-23444786-T-C not specified Uncertain significance (Apr 25, 2022)2285290
20-23444810-A-G not specified Uncertain significance (Aug 12, 2021)2375969
20-23444871-T-G not specified Uncertain significance (Oct 12, 2021)2255127

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
CSTL1protein_codingprotein_codingENST00000347397 35246
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
2.38e-80.043812528344611257480.00185
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense-0.04197776.01.010.00000386947
Missense in Polyphen3124.9651.2417317
Synonymous0.3113032.30.9300.00000187263
Loss of Function-1.02107.071.424.35e-766

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0002310.000231
Ashkenazi Jewish0.0004970.000496
East Asian0.01270.0125
Finnish0.00004620.0000462
European (Non-Finnish)0.0006330.000633
Middle Eastern0.01270.0125
South Asian0.004670.00465
Other0.001300.00130

dbNSFP

Source: dbNSFP

Recessive Scores

pRec
0.0878

Intolerance Scores

loftool
0.758
rvis_EVS
1.13
rvis_percentile_EVS
92.16

Haploinsufficiency Scores

pHI
0.118
hipred
N
hipred_score
0.112
ghis

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
gene_indispensability_pred
N
gene_indispensability_score
0.000684

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Cstl1
Phenotype

Gene ontology

Biological process
negative regulation of endopeptidase activity
Cellular component
extracellular region
Molecular function
cysteine-type endopeptidase inhibitor activity