CRYGN

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

Basic information

Region (hg38): 7:151428832-151440813

Links

ENSG00000127377 ∙ NCBI:155051 ∙ OMIM:609603 ∙ HGNC:20458 ∙ Uniprot:Q8WXF5 ∙ 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 CRYGN gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CRYGN 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			15		1	16
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	15	0	2

Variants in CRYGN

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

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

Position	Type	Phenotype	Significance	ClinVar
7-151430110-G-A		not specified	Uncertain significance (Mar 01, 2025)
7-151430147-G-C		not specified	Uncertain significance (Oct 05, 2023)
7-151430161-A-C		not specified	Uncertain significance (Jan 18, 2022)
7-151430178-G-A		not specified	Uncertain significance (Oct 20, 2024)
7-151436197-C-A		not specified	Uncertain significance (Nov 09, 2022)
7-151436226-A-G		not specified	Uncertain significance (May 21, 2024)
7-151436270-C-T		not specified	Uncertain significance (Oct 29, 2021)
7-151436272-C-G		not specified	Uncertain significance (Mar 02, 2023)
7-151436295-C-T			Benign (Dec 31, 2019)
7-151436306-A-G		not specified	Uncertain significance (Sep 03, 2024)
7-151438010-G-A		not specified	Uncertain significance (Feb 22, 2023)
7-151438045-C-T		not specified	Uncertain significance (Oct 13, 2023)
7-151438050-G-T		not specified	Uncertain significance (Feb 22, 2025)
7-151438093-C-T		not specified	Uncertain significance (Mar 01, 2025)
7-151438094-G-A		not specified	Uncertain significance (Feb 14, 2025)
7-151438100-C-T		not specified	Uncertain significance (Aug 04, 2021)
7-151438166-C-T		not specified	Uncertain significance (Feb 08, 2025)
7-151438189-T-G		not specified	Uncertain significance (Feb 19, 2025)
7-151438192-C-T		not specified	Uncertain significance (Mar 14, 2025)
7-151438234-T-C		not specified	Uncertain significance (Jan 24, 2023)
7-151438244-T-A		not specified	Uncertain significance (Dec 03, 2021)
7-151439903-C-T			Benign (Dec 31, 2019)
7-151439913-G-A		not specified	Uncertain significance (Nov 17, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CRYGN	protein_coding	protein_coding	ENST00000337323	4	11979

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.97e-7	0.116	125685	0	63	125748	0.000251

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.182	101	106	0.950	0.00000644	1215
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000297	0.000297
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000362	0.000360
Middle Eastern	0.0000544	0.0000544
South Asian	0.000294	0.000294
Other	0.000502	0.000489

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0957

Intolerance Scores

• loftool: 0.666
• rvis_EVS: -0.01
• rvis_percentile_EVS: 53.51

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.170
• ghis: 0.515

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.174

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Crygn
• Phenotype: nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); hearing/vestibular/ear phenotype