CRYZL1

crystallin zeta like 1

Basic information

Region (hg38): 21:33589341-33643926

Links

ENSG00000205758 ∙ NCBI:9946 ∙ OMIM:603920 ∙ HGNC:2420 ∙ Uniprot:O95825 ∙ 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 CRYZL1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CRYZL1 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			19			19
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	19	0	0

Variants in CRYZL1

This is a list of pathogenic ClinVar variants found in the CRYZL1 region.

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

Position	Type	Phenotype	Significance	ClinVar
21-33589838-T-G		not specified	Uncertain significance (Oct 28, 2024)
21-33589910-T-C		not specified	Uncertain significance (Jun 13, 2024)
21-33591182-C-A		not specified	Uncertain significance (Dec 10, 2024)
21-33595752-C-T		not specified	Uncertain significance (Jun 28, 2024)
21-33595793-G-A		not specified	Uncertain significance (Jun 24, 2022)
21-33599156-C-T		not specified	Uncertain significance (Sep 22, 2023)
21-33599171-C-A		not specified	Uncertain significance (Aug 28, 2023)
21-33599173-A-G		not specified	Uncertain significance (Aug 19, 2023)
21-33599219-C-T		not specified	Uncertain significance (Mar 12, 2024)
21-33602265-C-A		not specified	Uncertain significance (Feb 23, 2023)
21-33603416-C-G		not specified	Uncertain significance (Nov 07, 2023)
21-33603436-C-T		not specified	Uncertain significance (Dec 09, 2024)
21-33603489-C-T		not specified	Uncertain significance (Aug 28, 2024)
21-33603510-G-A		not specified	Uncertain significance (Feb 28, 2023)
21-33613586-C-T		not specified	Uncertain significance (Jul 12, 2023)
21-33621997-A-T		not specified	Uncertain significance (Jun 06, 2023)
21-33621998-T-C		not specified	Uncertain significance (Dec 26, 2023)
21-33622017-T-G		not specified	Uncertain significance (Sep 24, 2024)
21-33631520-G-T		not specified	Uncertain significance (Nov 06, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CRYZL1	protein_coding	protein_coding	ENST00000381554	12	54586

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.01e-9	0.425	125723	0	25	125748	0.0000994

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.761	149	178	0.839	0.00000823	2270
Missense in Polyphen		44	56.115	0.78411		755
Synonymous	-0.654	66	59.6	1.11	0.00000274	645
Loss of Function	0.984	16	20.8	0.767	9.63e-7	269

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.000139	0.000139
European (Non-Finnish)	0.000160	0.000149
Middle Eastern	0.00	0.00
South Asian	0.0000980	0.0000980
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0929

Intolerance Scores

• loftool: 0.639
• rvis_EVS: 0.19
• rvis_percentile_EVS: 67.03

Haploinsufficiency Scores

• pHI: 0.0987
• hipred: N
• hipred_score: 0.426
• ghis: 0.547

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.639

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cryzl1

Gene ontology

• Biological process: oxidation-reduction process;quinone metabolic process
• Cellular component: cytosol
• Molecular function: NADPH:quinone reductase activity;NADP binding