NANOGNB

Summary

NANOGNB (NANOG neighbor homeobox, HGNC:24958) is a protein-coding gene on chromosome 12p13.31, encoding NANOG neighbor homeobox (Q7Z5D8).

Predicted to enable DNA-binding transcription factor activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to be located in nucleus.

Source: NCBI Gene 360030 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 30 total
• MANE Select transcript: NM_001145465

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:24958
Approved symbol	NANOGNB
Name	NANOG neighbor homeobox
Location	12p13.31
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000205857
Ensembl biotype	protein_coding
OMIM	620692
Entrez	360030

Gene structure

Transcript identifiers

Ensembl transcripts: 2 — 2 protein_coding

ENST00000382119, ENST00000640040

RefSeq mRNA: 1 — MANE Select: NM_001145465 NM_001145465

CCDS: CCDS44826

Canonical transcript exons

ENST00000382119 — 4 exons

Exon	Start	End
ENSE00001490971	7773800	7774121
ENSE00001490972	7770439	7770518
ENSE00001490973	7769983	7770315
ENSE00001490974	7765216	7765387

Expression profiles

Bgee: expression breadth tissue_specific, 8 present calls, max score 79.43.

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	79.43	gold quality
colonic epithelium	UBERON:0000397	42.86	silver quality
bone marrow cell	CL:0002092	41.94	gold quality
lower esophagus mucosa	UBERON:0035834	41.56	silver quality
stromal cell of endometrium	CL:0002255	39.30	gold quality
granulocyte	CL:0000094	38.75	gold quality
ganglionic eminence	UBERON:0004023	37.62	silver quality
ventricular zone	UBERON:0003053	36.48	gold quality
cortical plate	UBERON:0005343	36.47	gold quality
liver	UBERON:0002107	32.30	gold quality
hindlimb stylopod muscle	UBERON:0004252	32.15	gold quality
primary visual cortex	UBERON:0002436	31.26	gold quality
leukocyte	CL:0000738	31.11	gold quality
superior frontal gyrus	UBERON:0002661	31.10	silver quality
sural nerve	UBERON:0015488	30.93	gold quality
monocyte	CL:0000576	30.76	gold quality
urinary bladder	UBERON:0001255	30.56	gold quality
lymph node	UBERON:0000029	30.42	silver quality
vermiform appendix	UBERON:0001154	30.05	silver quality
blood	UBERON:0000178	29.74	gold quality
right uterine tube	UBERON:0001302	29.64	gold quality
right lobe of liver	UBERON:0001114	29.09	gold quality
tonsil	UBERON:0002372	28.49	gold quality
duodenum	UBERON:0002114	28.14	gold quality
cortex of kidney	UBERON:0001225	28.11	gold quality
placenta	UBERON:0001987	27.90	silver quality
islet of Langerhans	UBERON:0000006	27.45	silver quality
metanephros cortex	UBERON:0010533	26.17	gold quality
kidney	UBERON:0002113	26.09	gold quality
muscle of leg	UBERON:0001383	26.04	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-GEOD-36552	yes	166.38
E-ANND-3	yes	3.61

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

19 targeting NANOGNB, 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-3163	100.00	77.23	8605
HSA-MIR-548AJ-3P	99.96	73.38	5345
HSA-MIR-548X-3P	99.96	73.38	5345
HSA-MIR-6755-5P	99.95	65.59	464
HSA-MIR-548J-3P	99.94	72.61	4881
HSA-MIR-548AE-3P	99.93	72.66	4867
HSA-MIR-548AH-3P	99.93	72.54	4872
HSA-MIR-548AM-3P	99.93	72.54	4872
HSA-MIR-548AQ-3P	99.93	72.66	4867
HSA-MIR-5582-3P	99.86	72.48	4221
HSA-MIR-139-5P	99.80	69.50	1399
HSA-MIR-136-5P	99.50	67.26	1153
HSA-MIR-578	99.46	68.36	1787
HSA-MIR-569	99.42	66.32	1009
HSA-MIR-4443	98.02	66.25	1928
HSA-MIR-7855-5P	97.39	67.18	925
HSA-MIR-3121-5P	97.30	66.62	1146
HSA-MIR-6841-5P	97.19	67.29	409
HSA-MIR-5195-5P	90.84	65.09	287

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	rims2b	ENSDARG00000102690
drosophila_melanogaster	Rim	FBGN0053547
caenorhabditis_elegans		WBGENE00006750

Paralogs (4): RIMS1 (ENSG00000079841), RIMS4 (ENSG00000101098), RIMS3 (ENSG00000117016), RIMS2 (ENSG00000176406)

Protein

Protein identifiers

NANOG neighbor homeobox — Q7Z5D8 (reviewed: Q7Z5D8)

Alternative names: Homeobox protein C14

All UniProt accessions (2): A0A1W2PR93, Q7Z5D8

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Nucleus.

RefSeq proteins (1): NP_001138937* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001356	HD	Domain
IPR009057	Homeodomain-like_sf	Homologous_superfamily

Pfam: PF00046

UniProt features (4 total): chain 1, DNA-binding region 1, region of interest 1, compositionally biased region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q7Z5D8-F1	68.24	0.01

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 16 (showing top): ACEVEDO_METHYLATED_IN_LIVER_CANCER_DN, GOMF_TRANSCRIPTION_REGULATOR_ACTIVITY, ZNF577_TARGET_GENES, MIR548AJ_3P_MIR548X_3P, MIR548AE_3P_MIR548AQ_3P, MIR548AH_3P_MIR548AM_3P, MIR548J_3P, MIR139_5P, MIR7855_5P, WP_PREIMPLANTATION_EMBRYO, ZNF623_TARGET_GENES, ZNF101_TARGET_GENES, ZNF555_TARGET_GENES, GOMF_DNA_BINDING_TRANSCRIPTION_FACTOR_ACTIVITY, PULVER_FOREY_PERTURB_ATTRITION_G1_S

GO Biological Process (1): regulation of transcription by RNA polymerase II (GO:0006357)

GO Molecular Function (2): DNA binding (GO:0003677), DNA-binding transcription factor activity (GO:0003700)

GO Cellular Component (1): nucleus (GO:0005634)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
regulation of DNA-templated transcription	2
transcription by RNA polymerase II	1
nucleic acid binding	1
transcription cis-regulatory region binding	1
transcription regulator activity	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

150 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
NANOGNB	DPRX	A6NFQ7	721
NANOGNB	TPRX1	Q8N7U7	667
NANOGNB	ANHX	E9PGG2	645
NANOGNB	ARGFX	A6NJG6	623
NANOGNB	DUXB	A0A1W2PPF3	609
NANOGNB	PRAMEF17	Q5VTA0	604
NANOGNB	LEUTX	A8MZ59	581
NANOGNB	PRAMEF20	Q5VT98	555
NANOGNB	DUXA	A6NLW8	548
NANOGNB	RHOXF2B	P0C7M4	480
NANOGNB	CT45A3	P0DMU6	418
NANOGNB	AICDA	Q9GZX7	395
NANOGNB	CT45A10	P0DMU9	392
NANOGNB	CT45A5	P0DMU8	372
NANOGNB	RHOXF2	Q9BQY4	370
NANOGNB	RAX2	Q96IS3	370

IntAct

2 interactions, top by confidence:

A	B	Type	Score
NANOGNB	PRKCSH	psi-mi:“MI:0915”(physical association)	0.400

BioGRID (3): NANOGNB (Two-hybrid), NANOGNB (Proximity Label-MS), NANOGNB (Cross-Linking-MS (XL-MS))

ESM2 similar proteins: A0A1B0GVG6, A6NE01, C0H3T6, G3UW99, P0C6L1, P0CT86, P11459, P19507, P31628, P32933, P32934, P32935, P33460, P34493, P46916, P84712, Q02838, Q03328, Q08561, Q09020, Q0ZNK1, Q27976, Q2TBV0, Q3E795, Q4V7B4, Q55H65, Q5H9L2, Q5MJ07, Q5MJ08, Q5MJ09, Q5SY13, Q5T7N2, Q6IPX3, Q6SJ84, Q6SJ91, Q7Z5D8, Q86TU6, Q8IZT9, Q8IZU0, Q8LAX3

Diamond homologs: P49796, Q05481, Q7Z5D8, Q96CB5, Q9NRJ1, A0A2R8Y7D0, Q9P1C3

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	26
Likely benign	2
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

362 predictions. Top by Δscore:

Variant	Effect	Δscore
12:7770148:G:GT	donor_gain	0.9900
12:7770149:A:T	donor_gain	0.9900
12:7770159:G:GT	donor_gain	0.9900
12:7770160:A:T	donor_gain	0.9900
12:7770438:GATAA:G	acceptor_gain	0.9900
12:7770166:G:T	donor_gain	0.9800
12:7770166:GAAAA:G	donor_gain	0.9800
12:7770201:A:G	donor_gain	0.9800
12:7770514:ATGAG:A	donor_loss	0.9800
12:7770515:TGAG:T	donor_loss	0.9800
12:7770516:GAGGT:G	donor_loss	0.9800
12:7770517:AG:A	donor_loss	0.9800
12:7770518:GG:G	donor_loss	0.9800
12:7770519:GTAAG:G	donor_loss	0.9800
12:7770520:T:TC	donor_loss	0.9800
12:7773796:ACAG:A	acceptor_loss	0.9800
12:7773797:CA:C	acceptor_loss	0.9800
12:7773798:A:AG	acceptor_gain	0.9800
12:7773798:AGA:A	acceptor_loss	0.9800
12:7773799:G:GG	acceptor_gain	0.9800
12:7773794:A:AG	acceptor_gain	0.9700
12:7773798:AGAT:A	acceptor_gain	0.9700
12:7773799:GATG:G	acceptor_gain	0.9700
12:7770112:G:GT	donor_gain	0.9600
12:7770521:AA:A	donor_loss	0.9600
12:7773795:A:G	acceptor_gain	0.9600
12:7773799:GAT:G	acceptor_gain	0.9600
12:7765384:CAAG:C	donor_loss	0.9500
12:7765385:AAGGT:A	donor_loss	0.9500
12:7765386:AGGT:A	donor_loss	0.9500

AlphaMissense

1248 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
12:7770451:T:C	F150L	0.972
12:7770453:T:A	F150L	0.972
12:7770453:T:G	F150L	0.972
12:7770241:T:C	F121L	0.970
12:7770243:T:A	F121L	0.970
12:7770243:T:G	F121L	0.970
12:7770289:T:C	F137L	0.942
12:7770291:T:A	F137L	0.942
12:7770291:T:G	F137L	0.942
12:7770448:T:A	W149R	0.940
12:7770448:T:C	W149R	0.940
12:7770295:T:C	F139L	0.939
12:7770297:T:A	F139L	0.939
12:7770297:T:G	F139L	0.939
12:7770242:T:C	F121S	0.915
12:7770450:G:C	W149C	0.913
12:7770450:G:T	W149C	0.913
12:7770452:T:C	F150S	0.901
12:7770234:G:C	W118C	0.895
12:7770234:G:T	W118C	0.895
12:7770440:T:A	I146K	0.874
12:7770465:G:C	R154S	0.870
12:7770465:G:T	R154S	0.870
12:7770440:T:C	I146T	0.866
12:7770284:T:C	L135P	0.858
12:7770303:G:A	M141I	0.856
12:7770303:G:C	M141I	0.856
12:7770303:G:T	M141I	0.856
12:7770315:G:C	Q145H	0.855
12:7770315:G:T	Q145H	0.855

dbSNP variants (sampled 300 via entrez): RS1000835827 (12:7773801 T>A), RS1000971987 (12:7768059 G>A), RS1001024289 (12:7768526 T>C), RS1001194405 (12:7766074 G>C,T), RS1001289355 (12:7773999 G>C), RS1001568968 (12:7766242 G>T), RS1001717234 (12:7772698 A>G), RS1001822098 (12:7772345 T>C), RS1002177342 (12:7768817 C>A), RS1002781734 (12:7763420 C>A), RS1002840378 (12:7771322 A>C,G,T), RS1003037829 (12:7766006 A>T), RS1003244282 (12:7763686 C>G,T), RS1003282182 (12:7767810 G>A), RS1003895223 (12:7773735 T>A,C)

Disease associations

OMIM: gene MIM:620692 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

4 total (human), top 4 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
hydroxyhydroquinone	increases expression	1
benzo(e)pyrene	increases methylation	1
Benzo(a)pyrene	affects methylation	1
Methapyrilene	increases methylation	1

Clinical trials (associated diseases)

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