CRYGN

Summary

CRYGN (crystallin gamma N, HGNC:20458) is a protein-coding gene on chromosome 7q36.1, encoding Gamma-crystallin N (Q8WXF5).

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.

Source: NCBI Gene 155051 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 44 total — 1 pathogenic
• MANE Select transcript: NM_144727

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:20458
Approved symbol	CRYGN
Name	crystallin gamma N
Location	7q36.1
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000127377
Ensembl biotype	protein_coding
OMIM	609603
Entrez	155051

Gene structure

Transcript identifiers

Ensembl transcripts: 6 — 4 protein_coding, 2 protein_coding_CDS_not_defined

ENST00000337323, ENST00000462809, ENST00000476631, ENST00000478106, ENST00000491928, ENST00000644350

RefSeq mRNA: 2 — MANE Select: NM_144727 NM_001308292, NM_144727

CCDS: CCDS5926, CCDS78289

Canonical transcript exons

ENST00000337323 — 4 exons

Exon	Start	End
ENSE00000000316	151439897	151440141
ENSE00001139656	151428832	151430180
ENSE00001139662	151437996	151438244
ENSE00003600753	151436180	151436325

Expression profiles

Bgee: expression breadth ubiquitous, 132 present calls, max score 88.32.

Top tissues by expression

233 total, by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
right lobe of thyroid gland	UBERON:0001119	88.32	gold quality
left lobe of thyroid gland	UBERON:0001120	86.90	gold quality
thyroid gland	UBERON:0002046	86.33	gold quality
decidua	UBERON:0002450	70.18	gold quality
buccal mucosa cell	CL:0002336	67.24	gold quality
endocervix	UBERON:0000458	64.65	gold quality
deltoid	UBERON:0001476	63.01	gold quality
popliteal artery	UBERON:0002250	63.00	gold quality
tibial artery	UBERON:0007610	63.00	gold quality
tendon of biceps brachii	UBERON:0008188	61.55	gold quality
left uterine tube	UBERON:0001303	60.82	gold quality
prefrontal cortex	UBERON:0000451	60.80	gold quality
right coronary artery	UBERON:0001625	60.71	gold quality
left coronary artery	UBERON:0001626	60.64	gold quality
body of uterus	UBERON:0009853	60.50	gold quality
aorta	UBERON:0000947	60.25	gold quality
coronary artery	UBERON:0001621	59.89	gold quality
ectocervix	UBERON:0012249	59.73	gold quality
biceps brachii	UBERON:0001507	59.10	gold quality
omental fat pad	UBERON:0010414	58.81	gold quality
peritoneum	UBERON:0002358	58.76	gold quality
secondary oocyte	CL:0000655	58.67	gold quality
tibial nerve	UBERON:0001323	58.47	gold quality
myometrium	UBERON:0001296	58.25	gold quality
uterine cervix	UBERON:0000002	58.23	gold quality
muscle layer of sigmoid colon	UBERON:0035805	57.90	gold quality
adipose tissue of abdominal region	UBERON:0007808	57.81	gold quality
anterior cingulate cortex	UBERON:0009835	57.04	gold quality
left ovary	UBERON:0002119	56.87	gold quality
lateral globus pallidus	UBERON:0002476	56.81	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-ANND-3	no	1.28

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

41 targeting CRYGN, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-6825-5P	99.96	69.81	3431
HSA-MIR-9718	99.94	68.91	918
HSA-MIR-3119	99.92	71.34	2390
HSA-MIR-4731-5P	99.89	67.23	2537
HSA-MIR-4492	99.87	68.25	3611
HSA-MIR-92A-2-5P	99.75	67.01	2164
HSA-MIR-3059-5P	99.70	69.93	2491
HSA-MIR-3660	99.68	67.33	1149
HSA-MIR-4526	99.68	67.07	1136
HSA-MIR-425-5P	99.59	67.67	900
HSA-MIR-24-3P	99.59	69.97	1934
HSA-MIR-6716-5P	99.56	68.62	1244
HSA-MIR-4649-3P	99.56	66.90	1783
HSA-MIR-4672	99.50	71.58	2893
HSA-MIR-569	99.42	66.32	1009
HSA-MIR-4505	99.27	67.81	2678
HSA-MIR-5787	99.22	67.86	2628
HSA-MIR-6868-5P	99.06	65.69	1284
HSA-MIR-4651	99.06	67.57	2002
HSA-MIR-1207-3P	98.99	66.22	1532
HSA-MIR-3196	98.96	63.91	326
HSA-MIR-608	98.93	67.83	2013
HSA-MIR-4709-3P	98.88	68.04	1594
HSA-MIR-29B-1-5P	98.86	68.35	1364
HSA-MIR-3180	98.46	64.68	348
HSA-MIR-3180-3P	98.46	64.68	348
HSA-MIR-6816-5P	98.46	64.35	364
HSA-MIR-628-5P	98.36	67.74	844
HSA-MIR-6881-3P	98.04	68.24	1777
HSA-MIR-4257	97.86	68.05	1190

Literature-anchored findings (GeneRIF, showing 1)

• gammaN-crystallin represents an intermediate in the evolution of beta and gamma crystallins. Crygn is expressed in mice and other species but may be a pseudogene in humans. (PMID:15853812)

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	crygn2	ENSDARG00000030411
danio_rerio	crygn1	ENSDARG00000102129
mus_musculus	Crygn	ENSMUSG00000038135
rattus_norvegicus	Crygn	ENSRNOG00000009226

Paralogs (14): CRYBG3 (ENSG00000080200), CRYBB3 (ENSG00000100053), CRYBB1 (ENSG00000100122), CRYBA1 (ENSG00000108255), CRYBG1 (ENSG00000112297), CRYGD (ENSG00000118231), CRYGC (ENSG00000163254), CRYBA2 (ENSG00000163499), CRYGA (ENSG00000168582), CRYBG2 (ENSG00000176092), CRYGB (ENSG00000182187), CRYBA4 (ENSG00000196431), CRYGS (ENSG00000213139), CRYBB2 (ENSG00000244752)

Protein

Protein identifiers

Gamma-crystallin N — Q8WXF5 (reviewed: Q8WXF5)

Alternative names: Gamma-N-crystallin

All UniProt accessions (4): Q8WXF5, A0A090N8I5, A0A1W2PRF4, A0A2R8Y702

UniProt curated annotations — full annotation on UniProt →

Subunit / interactions. Monomer.

Tissue specificity. Not specifically expressed in eye.

Similarity. Belongs to the beta/gamma-crystallin family.

Isoforms (2)

UniProt ID	Names	Canonical?
Q8WXF5-1	1	yes
Q8WXF5-2	2

RefSeq proteins (2): NP_001295221, NP_653328* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001064	Beta/gamma_crystallin	Domain
IPR011024	G_crystallin-like	Homologous_superfamily
IPR050252	Beta/Gamma-Crystallin	Family

Pfam: PF00030

UniProt features (8 total): domain 3, splice variant 2, chain 1, region of interest 1, compositionally biased region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8WXF5-F1	78.70	0.58

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 41 (showing top): GOBP_SENSORY_PERCEPTION_OF_LIGHT_STIMULUS, GOBP_SENSORY_PERCEPTION, GOBP_SENSORY_ORGAN_DEVELOPMENT, BREDEMEYER_RAG_SIGNALING_NOT_VIA_ATM_UP, GOBP_LENS_DEVELOPMENT_IN_CAMERA_TYPE_EYE, GOMF_STRUCTURAL_CONSTITUENT_OF_EYE_LENS, GOMF_STRUCTURAL_MOLECULE_ACTIVITY, MIKKELSEN_IPS_ICP_WITH_H3K4ME3_AND_H327ME3, MIKKELSEN_ES_ICP_WITH_H3K4ME3, GOBP_SENSORY_SYSTEM_DEVELOPMENT, ZWANG_TRANSIENTLY_UP_BY_2ND_EGF_PULSE_ONLY, H1_6_TARGET_GENES, HAND1_TARGET_GENES, NFE2L1_TARGET_GENES, MIR6825_5P

GO Biological Process (2): lens development in camera-type eye (GO:0002088), visual perception (GO:0007601)

GO Molecular Function (1): structural constituent of eye lens (GO:0005212)

GO Cellular Component (0):

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
camera-type eye development	1
anatomical structure development	1
sensory perception of light stimulus	1
structural molecule activity	1

Protein interactions and networks

STRING

1505 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CRYGN	GRIFIN	A4D1Z8	575
CRYGN	CRYAA	P02489	545
CRYGN	BFSP2	Q13515	526
CRYGN	WDR86	Q86TI4	503
CRYGN	LGSN	Q5TDP6	491
CRYGN	BFSP1	Q12934	454
CRYGN	CRYZL1	O95825	447
CRYGN	CRYAB	P02511	422
CRYGN	FAM174B	Q3ZCQ3	413
CRYGN	TBCCD1	Q9NVR7	404
CRYGN	CRYL1	Q9Y2S2	397
CRYGN	C7orf33	Q8WU49	394
CRYGN	DRC11L	A6NCM1	386
CRYGN	CRYM	Q14894	380
CRYGN	CNTN5	O94779	357

IntAct

3 interactions, top by confidence:

A	B	Type	Score
CRYGN	ALOX12B	psi-mi:“MI:0914”(association)	0.350
CRYGN	CST4	psi-mi:“MI:0914”(association)	0.350

BioGRID (11): CRYGN (Affinity Capture-RNA), DUSP3 (Affinity Capture-MS), ALOX12B (Affinity Capture-MS), CKM (Affinity Capture-MS), PIGR (Affinity Capture-MS), IGHA2 (Affinity Capture-MS), CST1 (Affinity Capture-MS), IGHA1 (Affinity Capture-MS), CST4 (Affinity Capture-MS), CST2 (Affinity Capture-MS), ZG16B (Affinity Capture-MS)

ESM2 similar proteins: A2IBY7, A2ICR5, A3RLD8, A3RLE2, A4L9I8, A4L9I9, O35486, P02525, P02526, P02528, P02529, P02531, P04342, P04344, P05813, P06504, P07315, P07316, P07317, P07320, P08209, P0C5E9, P10042, P10067, P10068, P10112, P11842, P11843, P11844, P14881, P22914, P23005, P26444, P49152, P53672, P53673, P55164, P56374, Q03740, Q28088

Diamond homologs: A2IBH5, A2IBY7, A2ICR5, A3RLD7, A3RLD8, A3RLE1, A3RLE2, A4L9I8, A4L9I9, A4QNB6, D3ZEG1, F6Q2R9, O35486, P02522, P02523, P02524, P02525, P02526, P02527, P02528, P02529, P02530, P02531, P04342, P04344, P04345, P05813, P06504, P07315, P07316, P07317, P07318, P07320, P07530, P08209, P0C5E9, P10042, P10043, P10044, P10065

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

44 variants total. Per-class counts are floors (≥ shown; pagination cap):

Classification	Count (floor)
Pathogenic	1
Likely pathogenic	0
Uncertain significance	35
Likely benign	0
Benign	2

Top pathogenic / likely-pathogenic (1)

Variant ID	HGVS	Classification
3148948	GRCh37/hg19 7q34-36.3(chr7:141690279-159119707)x3	Pathogenic

SpliceAI

771 predictions. Top by Δscore:

Variant	Effect	Δscore
7:151436178:A:AC	donor_gain	1.0000
7:151436178:ACGCT:A	donor_gain	1.0000
7:151436179:C:CC	donor_gain	1.0000
7:151436179:CG:C	donor_gain	1.0000
7:151436179:CGCT:C	donor_gain	1.0000
7:151436179:CGCTC:C	donor_gain	1.0000
7:151436329:C:CT	acceptor_gain	1.0000
7:151436329:C:T	acceptor_gain	1.0000
7:151436330:A:T	acceptor_gain	1.0000
7:151436335:C:CT	acceptor_gain	1.0000
7:151436335:C:T	acceptor_gain	1.0000
7:151436336:A:T	acceptor_gain	1.0000
7:151436339:C:CT	acceptor_gain	1.0000
7:151436340:A:T	acceptor_gain	1.0000
7:151438240:GTGAT:G	acceptor_gain	1.0000
7:151438241:TGAT:T	acceptor_gain	1.0000
7:151438242:GAT:G	acceptor_gain	1.0000
7:151438245:C:CC	acceptor_gain	1.0000
7:151439893:TCA:T	donor_loss	1.0000
7:151439894:CAC:C	donor_loss	1.0000
7:151439896:C:CA	donor_loss	1.0000
7:151432281:CCCAC:C	acceptor_gain	0.9900
7:151432282:CCACC:C	acceptor_gain	0.9900
7:151436226:AGCC:A	donor_gain	0.9900
7:151438241:TGATC:T	acceptor_gain	0.9900
7:151438242:GATCT:G	acceptor_gain	0.9900
7:151438243:AT:A	acceptor_gain	0.9900
7:151438243:ATC:A	acceptor_gain	0.9900
7:151438244:TC:T	acceptor_gain	0.9900
7:151438245:C:CA	acceptor_gain	0.9900

AlphaMissense

1228 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
7:151438110:G:C	F52L	0.978
7:151438110:G:T	F52L	0.978
7:151438112:A:G	F52L	0.978
7:151438043:A:G	W75R	0.957
7:151438043:A:T	W75R	0.957
7:151438095:G:C	F57L	0.954
7:151438095:G:T	F57L	0.954
7:151438097:A:G	F57L	0.954
7:151438161:A:C	F35L	0.948
7:151438161:A:T	F35L	0.948
7:151438163:A:G	F35L	0.948
7:151438218:G:C	F16L	0.942
7:151438218:G:T	F16L	0.942
7:151438220:A:G	F16L	0.942
7:151438080:G:C	F62L	0.938
7:151438080:G:T	F62L	0.938
7:151438082:A:G	F62L	0.938
7:151438121:A:G	W49R	0.930
7:151438121:A:T	W49R	0.930
7:151436296:G:C	F100L	0.929
7:151436296:G:T	F100L	0.929
7:151436298:A:G	F100L	0.929
7:151438115:A:G	C51R	0.928
7:151438075:A:G	L64S	0.916
7:151436311:G:C	F95L	0.915
7:151436311:G:T	F95L	0.915
7:151436313:A:G	F95L	0.915
7:151438050:G:C	F72L	0.914
7:151438050:G:T	F72L	0.914
7:151438052:A:G	F72L	0.914

dbSNP variants (sampled 300 via entrez): RS1000272069 (7:151431848 A>G,T), RS1000336052 (7:151442257 T>C), RS1000432180 (7:151435089 G>T), RS1000812327 (7:151433847 G>A), RS1000871518 (7:151441203 CAGGGACGGTCCTCCCT>C), RS1001320452 (7:151439195 A>G), RS1001376684 (7:151428782 G>GTCCATC), RS1001378741 (7:151441242 G>A), RS1001642513 (7:151430792 G>C), RS1001723273 (7:151429074 C>G), RS1001886775 (7:151435507 G>A), RS1001920370 (7:151438056 G>A), RS1002282415 (7:151429300 C>A), RS1002372793 (7:151437843 TGC>T), RS1002987671 (7:151436508 G>T)

Disease associations

OMIM: gene MIM:609603 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

1 associations (top):

Study	Trait	p-value
GCST010002_266	Refractive error	1.000000e-20

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

13 total (human), top 13 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	affects cotreatment, increases abundance, increases expression	1
manganese chloride	affects cotreatment, increases abundance, increases expression	1
4-aminophenylarsenoxide	decreases reaction, affects binding	1
(+)-JQ1 compound	decreases expression	1
Resveratrol	affects cotreatment, decreases expression	1
Arsenic Trioxide	affects binding, decreases reaction	1
Air Pollutants	increases abundance, increases expression	1
Arsenic	affects cotreatment, increases abundance, increases expression	1
Benzo(a)pyrene	increases methylation	1
Manganese	increases expression, affects cotreatment, increases abundance	1
Plant Extracts	affects cotreatment, decreases expression	1
Valproic Acid	increases methylation	1
Particulate Matter	increases abundance, increases expression	1

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.