CRYGN

protein-coding

crystallin gamma N, the group of Beta-gamma crystallins|MicroRNA protein coding host genes

Gene summary

This gene encodes a member of the crystallin family of proteins that are localized to the refractive structure of vertebrate eye lenses. The protein encoded by this gene is unique in that it has both beta and gamma crystallin protein motifs. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Apr 2015]

MANE transcript

NM_144727.3

Inheritance

—

ClinVar variants

U:39B:2

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1.19

Max pathogenic AF

—

Genomic locus

chr7:151,428,832-151,440,813

External References & Databases

Ensembl (ENSG00000127377)

Transcript & Mutation Effects

hg38 • Region Span ~12.0 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 CRYGN variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 34

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_144727.3. 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			2 clinvar		1 clinvar	3
missense			36 clinvar		1 clinvar	37
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	39	0	2	41

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 10 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_144727.3	RefSeq	NP_653328.1	4	MANE Select
ENST00000337323.3	Ensembl	ENSP00000338613.3	4	MANE Select
NM_001308292.1	RefSeq	NP_001295221.1	2	Standard
ENST00000478106.2	Ensembl	ENSP00000492574.2	2	Standard

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000337323
Coding exons: 4
Length: 11979
Individuals with no LoFs: 125685
Homozygous LoFs: 0
Heterozygous LoFs: 63
Defined: 125748
p: 0.000251

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.182	101	106	0.950	0.00000644	1215
Missense (PolyPhen)		33	35.264	0.9358		433
Synonymous	-0.412	44	40.7	1.08	0.00000268	321
Loss of Function	-0.475	9	7.59	1.19	4.88e-7	73

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00012	0.00012	rare
Latino/Admixed American	0.00017	0.00017	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000054	0.000054	rare
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.00036	0.00036	rare
South Asian	0.00029	0.00029	rare
Other	0.00050	0.00049	rare

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.0957

Intolerance Scores

LoFtool: 0.666
RVIS EVS: -0.01
RVIS percentile EVS: 53.51

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.174

Gene Damage Prediction

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