CSTL1

cystatin like 1, the group of Cystatins, type 2

Basic information

Region (hg38): 20:23426104-23444930

Links

ENSG00000125823 ∙ NCBI:128817 ∙ ∙ HGNC:15958 ∙ Uniprot:Q9H114 ∙ 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 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			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)
20-23440337-C-T		not specified	Uncertain significance (Jul 25, 2024)
20-23440373-A-T		not specified	Uncertain significance (May 14, 2024)
20-23440404-A-T		not specified	Uncertain significance (Jan 10, 2022)
20-23440411-C-A		not specified	Uncertain significance (Oct 12, 2024)
20-23440419-C-A		not specified	Uncertain significance (Jul 20, 2021)
20-23440435-C-A		not specified	Uncertain significance (Sep 08, 2024)
20-23440440-A-T		not specified	Uncertain significance (Aug 02, 2021)
20-23440475-A-G		not specified	Uncertain significance (Dec 31, 2023)
20-23440479-A-G		not specified	Uncertain significance (Dec 25, 2024)
20-23443938-C-T		not specified	Uncertain significance (Nov 21, 2024)
20-23443941-C-T		not specified	Uncertain significance (Jul 19, 2023)
20-23443971-T-C		not specified	Uncertain significance (Mar 16, 2022)
20-23444007-A-G		not specified	Likely benign (Jan 16, 2025)
20-23444786-T-C		not specified	Uncertain significance (Apr 25, 2022)
20-23444810-A-G		not specified	Uncertain significance (Aug 12, 2021)
20-23444871-T-G		not specified	Uncertain significance (Oct 12, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CSTL1	protein_coding	protein_coding	ENST00000347397	3	5246

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.38e-8	0.0438	125283	4	461	125748	0.00185

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0419	77	76.0	1.01	0.00000386	947
Missense in Polyphen		31	24.965	1.2417		317
Synonymous	0.311	30	32.3	0.930	0.00000187	263
Loss of Function	-1.02	10	7.07	1.42	4.35e-7	66

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000231	0.000231
Ashkenazi Jewish	0.000497	0.000496
East Asian	0.0127	0.0125
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000633	0.000633
Middle Eastern	0.0127	0.0125
South Asian	0.00467	0.00465
Other	0.00130	0.00130

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

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.000684

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cstl1

Gene ontology

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