CRYZ

crystallin zeta

Basic information

Region (hg38): 1:74705481-74733408

Links

ENSG00000116791 ∙ NCBI:1429 ∙ OMIM:123691 ∙ HGNC:2419 ∙ Uniprot:Q08257 ∙ 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 CRYZ gene.

• Inborn genetic diseases (10 variants)
• not provided (5 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CRYZ 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					1	1
missense			8		1	9
nonsense						0
start loss			1			1
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)				2		2
splice region						0
non coding			2			2
Total	0	0	11	2	2

Variants in CRYZ

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

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

Position	Type	Phenotype	Significance	ClinVar
1-74706373-A-G			Benign (Dec 31, 2019)
1-74706419-T-G		CRYZ-related disorder	Likely benign (Aug 21, 2022)
1-74706447-T-C		CRYZ-related disorder	Likely benign (May 17, 2022)
1-74706968-T-C		CRYZ-related disorder	Benign (Nov 21, 2019)
1-74707102-C-T			Likely benign (Jul 23, 2018)
1-74707105-T-C		not specified	Uncertain significance (Sep 17, 2021)
1-74707119-T-C		not specified	Uncertain significance (Dec 09, 2023)
1-74707146-A-C		not specified	Uncertain significance (Oct 12, 2021)
1-74707176-A-G		not specified	Uncertain significance (Jul 13, 2021)
1-74710111-A-G		not specified	Uncertain significance (Nov 10, 2022)
1-74710113-G-A		CRYZ-related disorder	Benign (Nov 06, 2019)
1-74710181-C-T		CRYZ-related disorder	Benign (Dec 31, 2019)
1-74710210-C-A		not specified	Uncertain significance (Dec 15, 2023)
1-74714616-G-A		not specified	Uncertain significance (Mar 07, 2024)
1-74719284-G-C		not specified	Uncertain significance (Jun 29, 2023)
1-74719347-C-G		not specified	Uncertain significance (Aug 17, 2022)
1-74719353-G-C		not specified	Uncertain significance (Nov 23, 2021)
1-74719373-C-T		CRYZ-related disorder	Likely benign (Oct 11, 2023)
1-74723167-T-A		not specified	Uncertain significance (Mar 14, 2023)
1-74723167-T-C		not specified	Uncertain significance (Oct 06, 2022)
1-74723218-C-T		CRYZ-related disorder • not specified	Conflicting classifications of pathogenicity (Feb 15, 2023)
1-74723262-G-T		CRYZ-related disorder	Likely benign (Sep 23, 2021)
1-74724821-T-G			Uncertain significance (Sep 23, 2017)
1-74733293-A-C		not specified	Uncertain significance (Jul 19, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CRYZ	protein_coding	protein_coding	ENST00000417775	8	27923

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.66e-23	0.0000144	125265	3	478	125746	0.00191

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.381	162	176	0.919	0.00000842	2111
Missense in Polyphen		43	51.258	0.83889		575
Synonymous	-0.0219	62	61.8	1.00	0.00000309	658
Loss of Function	-2.22	28	17.9	1.57	0.00000110	207

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00647	0.00621
Ashkenazi Jewish	0.00303	0.00298
East Asian	0.00447	0.00436
Finnish	0.000418	0.000370
European (Non-Finnish)	0.00147	0.00144
Middle Eastern	0.00447	0.00436
South Asian	0.00291	0.00278
Other	0.00118	0.00114

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Does not have alcohol dehydrogenase activity. Binds NADP and acts through a one-electron transfer process. Orthoquinones, such as 1,2-naphthoquinone or 9,10-phenanthrenequinone, are the best substrates (in vitro). May act in the detoxification of xenobiotics. Interacts with (AU)-rich elements (ARE) in the 3'-UTR of target mRNA species. Enhances the stability of mRNA coding for BCL2. NADPH binding interferes with mRNA binding. {ECO:0000269|PubMed:17497241, ECO:0000269|PubMed:20103721}.
• Pathway: oxidative stress induced gene expression via nrf2 (Consensus)

Recessive Scores

• pRec: 0.421

Intolerance Scores

• loftool: 0.997
• rvis_EVS: 0.46
• rvis_percentile_EVS: 78.59

Haploinsufficiency Scores

• pHI: 0.107
• hipred: N
• hipred_score: 0.294
• ghis: 0.495

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.514

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cryz

Gene ontology

• Biological process: visual perception;xenobiotic catabolic process;protein homotetramerization;oxidation-reduction process
• Cellular component: cytosol;extracellular exosome
• Molecular function: mRNA 3'-UTR binding;NADPH:quinone reductase activity;zinc ion binding;NADPH binding;NADH binding