CRYL1

crystallin lambda 1, the group of MicroRNA protein coding host genes

Basic information

Region (hg38): 13:20403665-20525873

Links

ENSG00000165475 ∙ NCBI:51084 ∙ OMIM:609877 ∙ HGNC:18246 ∙ Uniprot:Q9Y2S2 ∙ 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 CRYL1 gene.

• not provided (68 variants)
• Inborn genetic diseases (9 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CRYL1 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					3	3
missense			9			9
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					65	65
Total	0	0	9	0	68

Variants in CRYL1

This is a list of pathogenic ClinVar variants found in the CRYL1 region.

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

Position	Type	Phenotype	Significance	ClinVar
13-20404143-C-G		not specified	Uncertain significance (Dec 03, 2021)
13-20404365-C-T			Benign (May 10, 2021)
13-20404476-G-A			Benign (May 10, 2021)
13-20404525-T-C			Benign (May 10, 2021)
13-20404672-G-A		not specified	Uncertain significance (Dec 20, 2023)
13-20404686-A-T		CRYL1-related disorder	Likely benign (Jul 12, 2019)
13-20404690-T-C		not specified	Uncertain significance (Jun 22, 2023)
13-20404724-C-T		CRYL1-related disorder • not specified	Conflicting classifications of pathogenicity (Jun 11, 2021)
13-20404819-CAG-C			Benign (May 10, 2021)
13-20404888-G-A			Benign (May 10, 2021)
13-20404889-C-A			Benign (May 10, 2021)
13-20404965-G-A			Benign (May 10, 2021)
13-20413330-G-A		not specified	Uncertain significance (Dec 27, 2023)
13-20413354-C-A		not specified	Uncertain significance (Jul 26, 2023)
13-20413357-G-A		not specified	Uncertain significance (Dec 17, 2023)
13-20413369-T-C		not specified	Likely benign (Jan 17, 2024)
13-20413524-G-A			Benign (May 11, 2021)
13-20413589-A-G			Benign (May 10, 2021)
13-20414206-TAC-T			Benign (May 29, 2021)
13-20414206-TACAC-T			Benign (May 11, 2021)
13-20414206-TACACAC-T			Benign (May 11, 2021)
13-20414206-T-TAC			Benign (May 19, 2021)
13-20414254-T-TG			Benign (May 11, 2021)
13-20414255-T-G			Benign (May 11, 2021)
13-20414255-T-TTG			Benign (May 11, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CRYL1	protein_coding	protein_coding	ENST00000298248	8	122191

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000372	0.826	124720	0	74	124794	0.000297

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.403	169	184	0.916	0.00000993	2094
Missense in Polyphen		65	75.094	0.86558		844
Synonymous	0.439	68	72.8	0.934	0.00000445	608
Loss of Function	1.37	11	17.1	0.642	9.58e-7	187

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000188	0.000188
Ashkenazi Jewish	0.00	0.00
East Asian	0.000167	0.000167
Finnish	0.0000465	0.0000464
European (Non-Finnish)	0.000487	0.000486
Middle Eastern	0.000167	0.000167
South Asian	0.000229	0.000229
Other	0.000663	0.000660

dbNSFP

Source: dbNSFP

• Pathway: Pentose and glucuronate interconversions - Homo sapiens (human);Metabolism of carbohydrates;Metabolism;D-glucuronate degradation;Catabolism of glucuronate to xylulose-5-phosphate (Consensus)

Recessive Scores

• pRec: 0.142

Intolerance Scores

• loftool: 0.627
• rvis_EVS: -0.78
• rvis_percentile_EVS: 12.77

Haploinsufficiency Scores

• pHI: 0.130
• hipred: N
• hipred_score: 0.350
• ghis: 0.580

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.269

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cryl1

Gene ontology

• Biological process: fatty acid metabolic process;glucuronate catabolic process to xylulose 5-phosphate;oxidation-reduction process
• Cellular component: cytosol;extracellular exosome
• Molecular function: 3-hydroxyacyl-CoA dehydrogenase activity;protein homodimerization activity;L-gulonate 3-dehydrogenase activity;NAD+ binding