CHD9NB

Summary

CHD9NB (CHD9 neighbor, HGNC:53436) is a protein-coding gene on chromosome 16q12.2, encoding CHD9 neighbor protein (A0A1B0GV96).

At a glance

• MANE Select transcript: NM_001396020

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:53436
Approved symbol	CHD9NB
Name	CHD9 neighbor
Location	16q12.2
Locus type	gene with protein product
Status	Approved
Aliases	PR-lncRNA-1
Ensembl gene	ENSG00000277639
Ensembl biotype	protein_coding
Entrez	105371267

Gene structure

Transcript identifiers

Ensembl transcripts: 5 — 4 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000562178, ENST00000619363, ENST00000937481, ENST00000946301, ENST00000946302

RefSeq mRNA: 1 — MANE Select: NM_001396020 NM_001396020

CCDS: CCDS92160

Canonical transcript exons

ENST00000619363 — 3 exons

Exon	Start	End
ENSE00002626133	53047205	53047283
ENSE00003978134	53052761	53052897
ENSE00003978135	53041484	53044263

Expression profiles

Bgee: expression breadth ubiquitous, 185 present calls, max score 99.45.

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
epithelium of bronchus	UBERON:0002031	99.45	gold quality
bronchial epithelial cell	CL:0002328	99.43	gold quality
bronchus	UBERON:0002185	98.80	gold quality
right uterine tube	UBERON:0001302	98.34	gold quality
choroid plexus epithelium	UBERON:0003911	96.65	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	96.57	gold quality
mucosa of paranasal sinus	UBERON:0005030	95.16	gold quality
epithelium of nasopharynx	UBERON:0001951	94.62	gold quality
nasal cavity epithelium	UBERON:0005384	94.03	gold quality
cervix squamous epithelium	UBERON:0006922	90.02	silver quality
fallopian tube	UBERON:0003889	86.17	gold quality
oviduct epithelium	UBERON:0004804	85.97	gold quality
pancreatic ductal cell	CL:0002079	84.68	silver quality
metanephros cortex	UBERON:0010533	83.20	gold quality
trachea	UBERON:0003126	82.79	gold quality
nasal cavity mucosa	UBERON:0001826	82.24	gold quality
gall bladder	UBERON:0002110	81.22	gold quality
buccal mucosa cell	CL:0002336	81.18	silver quality
mucosa of transverse colon	UBERON:0004991	80.94	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	80.61	silver quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	79.17	gold quality
caput epididymis	UBERON:0004358	78.90	gold quality
type B pancreatic cell	CL:0000169	78.84	gold quality
olfactory bulb	UBERON:0002264	78.59	gold quality
germinal epithelium of ovary	UBERON:0001304	76.50	gold quality
nephron tubule	UBERON:0001231	76.40	gold quality
orbitofrontal cortex	UBERON:0004167	75.82	gold quality
cervix epithelium	UBERON:0004801	75.53	silver quality
rectum	UBERON:0001052	75.37	gold quality
mucosa of sigmoid colon	UBERON:0004993	75.26	gold quality

Single-cell (SCXA)

Detected in 5 experiment(s), a significant marker in 5.

Experiment	Marker?	Max mean expression
E-CURD-114	yes	64.43
E-MTAB-10287	yes	28.17
E-HCAD-1	yes	27.58
E-GEOD-130148	yes	13.12
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Gm19935	ENSMUSG00000110332
rattus_norvegicus		ENSRNOG00000078219

Protein

Protein identifiers

CHD9 neighbor protein — A0A1B0GV96 (reviewed: A0A1B0GV96)

All UniProt accessions (1): A0A1B0GV96

RefSeq proteins (1): NP_001382949* (*=MANE)

Domains & families (InterPro)

UniProt features (5 total): compositionally biased region 3, chain 1, region of interest 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-A0A1B0GV96-F1	60.52	0.00

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 25 (showing top): SENGUPTA_NASOPHARYNGEAL_CARCINOMA_DN, NAKAMURA_BRONCHIAL_AND_BRONCHIOLAR_EPITHELIA, DODD_NASOPHARYNGEAL_CARCINOMA_DN, ATF6_TARGET_GENES, E2F2_TARGET_GENES, MEF2D_TARGET_GENES, MIER1_TARGET_GENES, ZFHX3_TARGET_GENES, ZFP91_TARGET_GENES, ZNF184_TARGET_GENES, ZNF407_TARGET_GENES, ZNF512_TARGET_GENES, ZNF513_TARGET_GENES, ZBTB5_TARGET_GENES, ZSCAN5DP_TARGET_GENES

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (0):

Protein interactions and networks

STRING

0 interactions, top by confidence (×1000):

IntAct

0 interactions, top by confidence:

ESM2 similar proteins: A0A1B0GUA9, A0A1B0GV96, A4IFJ0, B3DGJ2, O43687, O55074, O70139, O75167, P04370, P0C8S0, P0C913, P0C914, P0CD96, P19103, P27775, P49342, P61925, P61926, P62025, P63248, P63249, Q04758, Q13522, Q29026, Q3SX13, Q3T0A6, Q3ZB98, Q4VC05, Q5FVI4, Q5R6X9, Q64256, Q6P3A1, Q71U53, Q7M2N1, Q7YQJ3, Q7YQJ4, Q8N111, Q8R409, Q8TAD7, Q8WMS3

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

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

Top pathogenic / likely-pathogenic (0)

SpliceAI

0 predictions. Top by Δscore:

AlphaMissense

333 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
16:53044152:A:G	C3R	0.727
16:53044155:C:A	G2W	0.722
16:53044141:G:C	S6R	0.713
16:53044141:G:T	S6R	0.713
16:53044143:T:G	S6R	0.713
16:53044155:C:G	G2R	0.698
16:53044155:C:T	G2R	0.698
16:53044151:C:G	C3S	0.693
16:53044152:A:T	C3S	0.693
16:53044150:G:C	C3W	0.679
16:53044147:G:C	H4Q	0.589
16:53044147:G:T	H4Q	0.589

dbSNP variants (sampled 300 via entrez): RS1000280197 (16:53037360 T>C), RS1000467216 (16:53037084 C>T), RS1000797840 (16:53038581 C>T), RS1001386233 (16:53044311 C>T), RS1001483828 (16:53044823 C>T), RS1001684636 (16:53042836 A>C), RS1001785172 (16:53037118 TA>T), RS1001822637 (16:53046480 C>T), RS1001853712 (16:53046931 G>A), RS1001857018 (16:53036734 A>G), RS1002335186 (16:53053551 G>A,T), RS1002516981 (16:53035680 C>T), RS1002563161 (16:53054861 G>A), RS1002608913 (16:53035452 T>C), RS1002658210 (16:53054161 T>G)

Disease associations

OMIM: gene `` | 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

6 total (human), top 6 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
sotorasib	affects cotreatment, increases expression	1
trametinib	affects cotreatment, increases expression	1
NVP-BKM120	affects cotreatment, increases expression	1
Air Pollutants	increases abundance, increases expression	1
Smoke	increases expression, increases abundance	1
Okadaic Acid	decreases expression	1

Clinical trials (associated diseases)

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