CRYL1

protein-coding

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

Gene summary

The uronate cycle functions as an alternative glucose metabolic pathway, accounting for about 5% of daily glucose catabolism. The product of this gene catalyzes the dehydrogenation of L-gulonate into dehydro-L-gulonate in the uronate cycle. The enzyme requires NAD(H) as a coenzyme, and is inhibited by inorganic phosphate. A similar gene in the rabbit is thought to serve a structural role in the lens of the eye. [provided by RefSeq, Jul 2008]

MANE transcript

NM_015974.3

Inheritance

—

ClinVar variants

U:44B:9

Top phenotype

CRYL1-related disorder

gnomAD constraint

pLI —, LoF o/e 0.64

Max pathogenic AF

—

Genomic locus

chr13:20,403,666-20,525,873

External References & Databases

Ensembl (ENSG00000165475)

Transcript & Mutation Effects

hg38 • Region Span ~122.2 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to CRYL1 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 44

not providedTotal: 10

CRYL1-related disorderTotal: 5

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_015974.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar	2 clinvar	2 clinvar	5
missense			41 clinvar	4 clinvar	1 clinvar	46
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	44	6	3	53

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 57 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_015974.3	RefSeq	NP_057058.2	8	MANE Select
ENST00000298248.12	Ensembl	ENSP00000298248.7	8	MANE Select
NM_001363647.2	RefSeq	NP_001350576.1	7	Standard
ENST00000382812.5	Ensembl	ENSP00000372262.1	7	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

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

Biological Process

fatty acid metabolic process
glucuronate catabolic process to xylulose 5-phosphate
oxidation-reduction process

Molecular Function

3-hydroxyacyl-CoA dehydrogenase activity
protein homodimerization activity
L-gulonate 3-dehydrogenase activity
NAD+ binding

Cellular Component

cytosol
extracellular exosome

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000298248
Coding exons: 8
Length: 122191
Individuals with no LoFs: 124720
Homozygous LoFs: 0
Heterozygous LoFs: 74
Defined: 124794
p: 0.000297

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.403	169	184	0.916	0.00000993	2094
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00013	0.00013	rare
Latino/Admixed American	0.000058	0.000058	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00017	0.00017	rare
Finnish	0.000047	0.000046	rare
European (Non-Finnish)	0.00049	0.00049	rare
South Asian	0.00023	0.00023	rare
Other	0.00066	0.00066	rare

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.142

Intolerance Scores

LoFtool: 0.627
RVIS EVS: -0.78
RVIS percentile EVS: 12.77

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.269

Gene Damage Prediction

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