CRYBG2

Summary

CRYBG2 (crystallin beta-gamma domain containing 2, HGNC:17295) is a protein-coding gene on chromosome 1p36.11, encoding Beta/gamma crystallin domain-containing protein 2 (Q8N1P7).

Predicted to enable carbohydrate binding activity.

Source: NCBI Gene 55057 — RefSeq curated summary.

At a glance

• GWAS associations: 5
• Clinical variants (ClinVar): 333 total
• MANE Select transcript: NM_001039775

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:17295
Approved symbol	CRYBG2
Name	crystallin beta-gamma domain containing 2
Location	1p36.11
Locus type	gene with protein product
Status	Approved
Aliases	FLJ38020
Ensembl gene	ENSG00000176092
Ensembl biotype	protein_coding
OMIM	619765
Entrez	55057

Gene structure

Transcript identifiers

Ensembl transcripts: 10 — 5 protein_coding_CDS_not_defined, 3 protein_coding, 2 retained_intron

ENST00000308182, ENST00000374207, ENST00000374208, ENST00000374211, ENST00000429942, ENST00000475866, ENST00000520372, ENST00000522923, ENST00000522993, ENST00000640960

RefSeq mRNA: 1 — MANE Select: NM_001039775 NM_001039775

Canonical transcript exons

ENST00000308182 — 20 exons

Exon	Start	End
ENSE00001159424	26328734	26328873
ENSE00001208043	26338351	26338477
ENSE00001231582	26328209	26328332
ENSE00001231635	26339290	26339429
ENSE00001462784	26321865	26322056
ENSE00001715571	26343745	26346712
ENSE00001911784	26354036	26354130
ENSE00003468900	26324152	26324310
ENSE00003476450	26336841	26336980
ENSE00003502259	26336095	26336207
ENSE00003524224	26322164	26322323
ENSE00003576219	26331489	26331618
ENSE00003587063	26336606	26336732
ENSE00003589012	26336338	26336370
ENSE00003589525	26337538	26337674
ENSE00003641235	26337253	26337379
ENSE00003666345	26338012	26338047
ENSE00003711961	26343047	26343159
ENSE00003724301	26342754	26342883
ENSE00003752245	26343246	26343293

Expression profiles

Bgee: expression breadth ubiquitous, 212 present calls, max score 99.12.

FANTOM5 (CAGE): breadth broad, TPM avg 1.8557 / max 91.1624, expressed in 455 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter ID	TPM avg	Samples expressed
11168	1.0949	207
11167	0.6067	279
11170	0.1178	15
11169	0.0264	10
11171	0.0098	5

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
lower esophagus mucosa	UBERON:0035834	99.12	gold quality
esophagus mucosa	UBERON:0002469	96.63	gold quality
skin of abdomen	UBERON:0001416	93.85	gold quality
cervix squamous epithelium	UBERON:0006922	93.63	gold quality
esophagus squamous epithelium	UBERON:0006920	93.20	gold quality
squamous epithelium	UBERON:0006914	92.91	gold quality
skin of leg	UBERON:0001511	92.65	gold quality
buccal mucosa cell	CL:0002336	92.48	gold quality
epithelium of esophagus	UBERON:0001976	92.32	gold quality
pharyngeal mucosa	UBERON:0000355	91.59	gold quality
gingival epithelium	UBERON:0001949	91.42	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	91.14	gold quality
gingiva	UBERON:0001828	90.34	gold quality
amniotic fluid	UBERON:0000173	90.25	gold quality
zone of skin	UBERON:0000014	90.12	gold quality
oral cavity	UBERON:0000167	87.47	gold quality
tongue squamous epithelium	UBERON:0006919	86.94	gold quality
cervix epithelium	UBERON:0004801	86.12	gold quality
mucosa of transverse colon	UBERON:0004991	85.69	gold quality
placenta	UBERON:0001987	85.62	gold quality
vagina	UBERON:0000996	84.00	gold quality
pancreatic ductal cell	CL:0002079	83.42	silver quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	82.99	gold quality
type B pancreatic cell	CL:0000169	82.52	silver quality
diaphragm	UBERON:0001103	80.53	gold quality
olfactory bulb	UBERON:0002264	79.71	gold quality
duodenum	UBERON:0002114	79.57	gold quality
palpebral conjunctiva	UBERON:0001812	77.60	gold quality
granulocyte	CL:0000094	77.47	gold quality
mammalian vulva	UBERON:0000997	76.61	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 2.

Experiment	Marker?	Max mean expression
E-GEOD-111727	yes	253.31
E-ANND-3	yes	4.96

Regulation

Is transcription factor: no

Literature-anchored findings (GeneRIF, showing 2)

• The apparent occurrence of an unusual TG 3’ splice site in intron 2 is critically discussed. (PMID:17672918)
• Absent in melanoma 1-like (AIM1L) serves as a novel candidate for overall survival in hepatocellular carcinoma. (PMID:34130591)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	prdm1b	ENSDARG00000098777
mus_musculus	Crybg2	ENSMUSG00000012123
rattus_norvegicus	Crybg2	ENSRNOG00000057957

Paralogs (14): CRYBG3 (ENSG00000080200), CRYBB3 (ENSG00000100053), CRYBB1 (ENSG00000100122), CRYBA1 (ENSG00000108255), CRYBG1 (ENSG00000112297), CRYGD (ENSG00000118231), CRYGN (ENSG00000127377), CRYGC (ENSG00000163254), CRYBA2 (ENSG00000163499), CRYGA (ENSG00000168582), CRYGB (ENSG00000182187), CRYBA4 (ENSG00000196431), CRYGS (ENSG00000213139), CRYBB2 (ENSG00000244752)

Protein

Protein identifiers

Beta/gamma crystallin domain-containing protein 2 — Q8N1P7 (reviewed: Q8N1P7)

Alternative names: Absent in melanoma 1-like protein

All UniProt accessions (3): E7ET48, Q8N1P7, J3KQW1

UniProt curated annotations — full annotation on UniProt →

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

RefSeq proteins (1): NP_001034864* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000772	Ricin_B_lectin	Domain
IPR001064	Beta/gamma_crystallin	Domain
IPR011024	G_crystallin-like	Homologous_superfamily
IPR035992	Ricin_B-like_lectins	Homologous_superfamily
IPR050252	Beta/Gamma-Crystallin	Family

Pfam: PF00030, PF00652

UniProt features (33 total): domain 13, compositionally biased region 10, region of interest 8, chain 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8N1P7-F1	55.71	0.27

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 102 (showing top): GSE45365_CD8A_DC_VS_CD11B_DC_IFNAR_KO_MCMV_INFECTION_DN, TGGTGCT_MIR29A_MIR29B_MIR29C, JAEGER_METASTASIS_DN, IVANOVA_HEMATOPOIESIS_LATE_PROGENITOR, NKX62_Q2, RICKMAN_TUMOR_DIFFERENTIATED_WELL_VS_POORLY_DN, HNF4_01, TIEN_INTESTINE_PROBIOTICS_24HR_UP, YYCATTCAWW_UNKNOWN, ACEVEDO_METHYLATED_IN_LIVER_CANCER_DN, CP2_01, TAATTA_CHX10_01, CHARAFE_BREAST_CANCER_LUMINAL_VS_MESENCHYMAL_UP, GAVIN_FOXP3_TARGETS_CLUSTER_P2, SENGUPTA_EBNA1_ANTICORRELATED

GO Biological Process (0):

GO Molecular Function (1): carbohydrate binding (GO:0030246)

GO Cellular Component (0):

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
binding	1

Protein interactions and networks

STRING

782 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CRYBG2	TMEM191C	A6NGB0	700
CRYBG2	LKAAEAR1	Q8TD35	507
CRYBG2	NOP16	Q9Y3C1	455
CRYBG2	PRSS48	Q7RTY5	440
CRYBG2	OR8G1	Q15617	430
CRYBG2	ZNF280C	Q8ND82	411
CRYBG2	GXYLT1	Q4G148	397
CRYBG2	OR11G2	Q8NGC1	395
CRYBG2	ZNF681	Q96N22	393
CRYBG2	OR51F1	A6NGY5	392
CRYBG2	PIGW	Q7Z7B1	373
CRYBG2	LYPD2	Q6UXB3	364
CRYBG2	OR8G5	Q8NG78	360
CRYBG2	POM121L2	Q96KW2	353
CRYBG2	IYD	Q6PHW0	352

IntAct

4 interactions, top by confidence:

A	B	Type	Score
ATG16L1	ESYT2	psi-mi:“MI:0914”(association)	0.350
CRYBG2	DDX3Y	psi-mi:“MI:0914”(association)	0.350
CRYBG2	CORO1A	psi-mi:“MI:0914”(association)	0.350

BioGRID (30): AIM1L (Affinity Capture-MS), KLHDC3 (Affinity Capture-MS), SATB2 (Affinity Capture-MS), CSRP2BP (Affinity Capture-MS), L3MBTL2 (Affinity Capture-MS), ZZZ3 (Affinity Capture-MS), PCGF6 (Affinity Capture-MS), LRIF1 (Affinity Capture-MS), HELZ (Affinity Capture-MS), RPL23 (Affinity Capture-MS), DDX3Y (Affinity Capture-MS), MCM8 (Affinity Capture-MS), ATXN2 (Affinity Capture-MS), MAP3K7 (Affinity Capture-MS), YEATS2 (Affinity Capture-MS)

ESM2 similar proteins: A0A0J9YXV3, A0A172M4N0, A2VE23, A5PL33, C7EMF5, E7EW31, F1NSM7, I3L273, O15027, O48582, O55189, O55196, O97939, P0C671, P0DV77, P14138, Q14D33, Q1XI13, Q28989, Q3B7M4, Q4R729, Q5R7U0, Q5SWP3, Q62840, Q63003, Q6E0U4, Q6H236, Q6NUN9, Q6UXA7, Q7Z2K8, Q86UU5, Q8BM15, Q8K4E0, Q8K4L6, Q8N1P7, Q8N3D4, Q96D09, Q96JG9, Q9BGL9, Q9D7G9

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, P10065, P10066

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	264
Likely benign	38
Benign	1

Top pathogenic / likely-pathogenic (0)

SpliceAI

2894 predictions. Top by Δscore:

Variant	Effect	Δscore
1:26322162:AC:A	donor_gain	1.0000
1:26322163:CC:C	donor_gain	1.0000
1:26324306:CGGCG:C	acceptor_gain	1.0000
1:26324308:GCG:G	acceptor_gain	1.0000
1:26324309:CG:C	acceptor_gain	1.0000
1:26324309:CGC:C	acceptor_gain	1.0000
1:26324311:C:CC	acceptor_gain	1.0000
1:26328732:A:AC	donor_gain	1.0000
1:26328733:C:CC	donor_gain	1.0000
1:26328843:CA:C	acceptor_gain	1.0000
1:26328872:TG:T	acceptor_gain	1.0000
1:26328874:C:CC	acceptor_gain	1.0000
1:26328882:C:CT	acceptor_gain	1.0000
1:26328882:C:T	acceptor_gain	1.0000
1:26328883:A:T	acceptor_gain	1.0000
1:26331614:TCCAG:T	acceptor_gain	1.0000
1:26331615:CCAG:C	acceptor_gain	1.0000
1:26331615:CCAGC:C	acceptor_gain	1.0000
1:26331616:CAG:C	acceptor_gain	1.0000
1:26331616:CAGC:C	acceptor_gain	1.0000
1:26331619:C:CC	acceptor_gain	1.0000
1:26336090:CTCA:C	donor_loss	1.0000
1:26336091:TCACC:T	donor_loss	1.0000
1:26336092:CAC:C	donor_loss	1.0000
1:26336093:A:C	donor_loss	1.0000
1:26336203:TGAAT:T	acceptor_gain	1.0000
1:26336206:AT:A	acceptor_gain	1.0000
1:26336208:C:CC	acceptor_gain	1.0000
1:26336209:T:A	acceptor_loss	1.0000
1:26336215:C:CT	acceptor_gain	1.0000

AlphaMissense

10661 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
1:26322230:A:G	W1611R	0.999
1:26322230:A:T	W1611R	0.999
1:26324184:A:G	W1569R	0.999
1:26324184:A:T	W1569R	0.999
1:26328262:A:G	W1509R	0.999
1:26328262:A:T	W1509R	0.999
1:26321988:A:G	W1656R	0.998
1:26321988:A:T	W1656R	0.998
1:26336731:A:G	W1305R	0.998
1:26336731:A:T	W1305R	0.998
1:26322165:C:A	K1632N	0.997
1:26322165:C:G	K1632N	0.997
1:26322228:C:A	W1611C	0.997
1:26322228:C:G	W1611C	0.997
1:26322260:A:G	W1601R	0.997
1:26322260:A:T	W1601R	0.997
1:26328260:C:A	W1509C	0.997
1:26328260:C:G	W1509C	0.997
1:26328331:A:G	W1486R	0.997
1:26328331:A:T	W1486R	0.997
1:26331617:A:G	W1396R	0.997
1:26331617:A:T	W1396R	0.997
1:26336653:A:G	W1331R	0.997
1:26336653:A:T	W1331R	0.997
1:26337378:A:G	W1216R	0.997
1:26337378:A:T	W1216R	0.997
1:26322258:C:A	W1601C	0.996
1:26322258:C:G	W1601C	0.996
1:26322270:C:A	K1597N	0.996
1:26322270:C:G	K1597N	0.996

dbSNP variants (sampled 300 via entrez): RS1000363802 (1:26344429 G>A), RS1000379511 (1:26331320 A>T), RS1000565221 (1:26354822 G>A), RS1000611625 (1:26350015 A>G), RS1000807790 (1:26339855 A>T), RS1000912675 (1:26340618 T>C), RS1000962699 (1:26334308 C>T), RS1000987861 (1:26336369 AC>A), RS1001002032 (1:26351773 C>A,T), RS1001211724 (1:26348659 G>A,T), RS1001260058 (1:26340146 A>G), RS1001413232 (1:26343640 C>G), RS1001452995 (1:26347542 G>A), RS1001574081 (1:26330783 C>T), RS1001627890 (1:26331164 G>A)

Disease associations

OMIM: gene MIM:619765 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

5 associations (top):

Study	Trait	p-value
GCST001762_803	Obesity-related traits	5.000000e-06
GCST004625_1	Monocyte count	8.000000e-12
GCST010320_25	PR interval	3.000000e-09
GCST010321_171	PR interval	2.000000e-09
GCST90002393_118	Monocyte count	7.000000e-29

EFO canonical traits (3, from GWAS)

EFO ID	Trait name
EFO:0003940	physical activity
EFO:0005091	monocyte count
EFO:0004462	PR interval

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

PharmGKB clinical annotations

1 annotations.

Variant	Type	Level	Drugs	Phenotypes
rs36024412	Toxicity	3	opioids	Nausea;Vomiting

PharmGKB variants

1 variants.

Variant	Genes	Level	Score	#Clin annots	Drugs
rs36024412	CRYBG2	3	0.00	1	opioids

CTD chemical–gene interactions

49 total (human), top 30 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	increases expression, affects expression, increases methylation, affects cotreatment	7
bisphenol A	decreases expression, decreases methylation	3
sodium arsenite	decreases expression, increases expression	2
Benzo(a)pyrene	decreases expression, increases expression	2
Estradiol	decreases expression, affects cotreatment	2
Progesterone	decreases expression, increases expression	2
Cyclosporine	increases expression	2
dicrotophos	increases expression	1
2,4,6-tribromophenol	increases expression	1
methyleugenol	increases expression	1
triphenyl phosphate	affects expression	1
propionaldehyde	increases expression	1
pyrogallol 1,3-dimethyl ether	affects cotreatment, affects localization, decreases expression, increases expression	1
decabromobiphenyl ether	increases expression	1
beta-lapachone	increases expression	1
butyraldehyde	increases expression	1
tetrabromobisphenol A	increases expression	1
tobacco tar	decreases expression	1
hydroquinone	increases expression	1
pentanal	increases expression	1
entinostat	increases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, increases expression	1
dorsomorphin	increases expression, affects cotreatment	1
pentabrominated diphenyl ether 100	increases expression	1
hexabrominated diphenyl ether 153	increases expression	1
Aldehydes	increases expression	1
Diethylhexyl Phthalate	decreases expression	1
Ethyl Methanesulfonate	increases expression	1
Formaldehyde	increases expression	1
Furaldehyde	increases expression, affects cotreatment, decreases expression, affects localization	1

Clinical trials (associated diseases)

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