CXorf49C

Summary

CXorf49C (chromosome X open reading frame 49C, HGNC:53552) is a protein-coding gene on chromosome Xq13.1, encoding Uncharacterized protein CXorf49C (A0A1B0GWI6).

At a glance

• Clinical variants (ClinVar): 5 total — 1 pathogenic
• MANE Select transcript: NM_001323075

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:53552
Approved symbol	CXorf49C
Name	chromosome X open reading frame 49C
Location	Xq13.1
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000283599
Ensembl biotype	protein_coding
Entrez	101059915

Gene structure

Transcript identifiers

Ensembl transcripts: 2 — 2 protein_coding

ENST00000636096, ENST00000636797

RefSeq mRNA: 1 — MANE Select: NM_001323075 NM_001323075

CCDS: CCDS87758

Canonical transcript exons

ENST00000636096 — 6 exons

Exon	Start	End
ENSE00003795491	71667546	71669039
ENSE00003796260	71669559	71669715
ENSE00003796381	71670258	71670334
ENSE00003798174	71670612	71670657
ENSE00003803383	71671207	71671248
ENSE00003997455	71671354	71671527

Expression profiles

Bgee: expression breadth broad, 24 present calls, max score 83.83.

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	83.83	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	80.73	gold quality
right testis	UBERON:0004534	75.25	gold quality
left testis	UBERON:0004533	74.56	gold quality
testis	UBERON:0000473	74.21	gold quality
superior frontal gyrus	UBERON:0002661	46.53	silver quality
Brodmann (1909) area 9	UBERON:0013540	45.56	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	45.23	gold quality
anterior cingulate cortex	UBERON:0009835	45.01	gold quality
right frontal lobe	UBERON:0002810	44.75	gold quality
frontal cortex	UBERON:0001870	43.34	gold quality
prefrontal cortex	UBERON:0000451	42.17	silver quality
cerebral cortex	UBERON:0000956	42.07	gold quality
amygdala	UBERON:0001876	41.38	gold quality
temporal lobe	UBERON:0001871	41.22	gold quality
bone marrow cell	CL:0002092	40.65	gold quality
primary visual cortex	UBERON:0002436	40.35	gold quality
sural nerve	UBERON:0015488	38.97	gold quality
lower esophagus mucosa	UBERON:0035834	37.83	gold quality
colonic epithelium	UBERON:0000397	37.20	gold quality
ventricular zone	UBERON:0003053	36.48	gold quality
cortical plate	UBERON:0005343	36.47	gold quality
bone marrow	UBERON:0002371	36.38	gold quality
skeletal muscle tissue	UBERON:0001134	36.34	gold quality
apex of heart	UBERON:0002098	35.74	gold quality
hindlimb stylopod muscle	UBERON:0004252	35.61	gold quality
ganglionic eminence	UBERON:0004023	35.49	gold quality
muscle tissue	UBERON:0002385	34.99	gold quality
metanephros cortex	UBERON:0010533	34.59	gold quality
cortex of kidney	UBERON:0001225	34.51	silver quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	1.63

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

8 targeting CXorf49C, 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-4425	100.00	67.59	1049
HSA-MIR-298	99.63	67.56	1916
HSA-MIR-8065	99.19	70.38	1289
HSA-MIR-1843	98.97	66.07	838
HSA-MIR-4802-5P	98.97	66.26	833
HSA-MIR-203B-3P	97.82	66.27	979
HSA-MIR-549A-5P	96.35	68.08	587
HSA-MIR-6805-5P	95.79	64.86	670

Cross-species orthologs

8 orthologs

Organism	Symbol	Gene ID
mus_musculus	Gm4779	ENSMUSG00000045010
mus_musculus	8030474K03Rik	ENSMUSG00000046774
mus_musculus	4933412E24Rik	ENSMUSG00000071749
mus_musculus	Gm3858	ENSMUSG00000118638
rattus_norvegicus	4933412E24Rikl	ENSRNOG00000004914
rattus_norvegicus	Cxhxorf49B	ENSRNOG00000025200
rattus_norvegicus	Cxhxorf49	ENSRNOG00000025211
rattus_norvegicus	Cxhxorf49l1	ENSRNOG00000060462

Paralogs (2): CXorf49B (ENSG00000215113), CXorf49 (ENSG00000215115)

Protein

Protein identifiers

Uncharacterized protein CXorf49C — A0A1B0GWI6 (reviewed: A0A1B0GWI6)

All UniProt accessions (2): A0A1B0GWI6, A0A1B0GV59

RefSeq proteins (1): NP_001310004* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR027822	CXorf49	Family

Pfam: PF15483

UniProt features (1 total): chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

No AlphaFold model available for A0A1B0GWI6 — AlphaFold DB does not currently provide models for proteins above ~3000 aa.

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 0 (showing top):

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (0):

Protein interactions and networks

STRING

190 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CXorf49C	MPPED1	O15442	513
CXorf49C	USP50	Q70EL3	449
CXorf49C	C1QTNF9	P0C862	447
CXorf49C	KRTDAP	P60985	446
CXorf49C	PLA2G3	Q9NZ20	425
CXorf49C	MYZAP	P0CAP1	368
CXorf49C	GTF2I	P78347	306
CXorf49C	WFIKKN2	Q8TEU8	269
CXorf49C	ETV5	P41161	255
CXorf49C	IGFBPL1	Q8WX77	253
CXorf49C	GPR174	Q9BXC1	248
CXorf49C	DUSP26	Q9BV47	226
CXorf49C	TIAM1	Q13009	226
CXorf49C	DUSP28	Q4G0W2	226
CXorf49C	MEN1	O00255	222

IntAct

0 interactions, top by confidence:

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	1
Likely pathogenic	0
Uncertain significance	0
Likely benign	4
Benign	0

Top pathogenic / likely-pathogenic (1)

Variant ID	HGVS	Classification
148479	GRCh38/hg38 Xq11.1-28(chrX:62561604-156003242)x3	Pathogenic

SpliceAI

0 predictions. Top by Δscore:

AlphaMissense

3350 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
X:71670643:T:C	L501P	0.897
X:71668824:T:C	F341L	0.847
X:71668826:T:A	F341L	0.847
X:71668826:T:G	F341L	0.847
X:71671233:T:C	F515L	0.847
X:71671235:C:A	F515L	0.847
X:71671235:C:G	F515L	0.847
X:71670326:T:C	C488R	0.843
X:71667978:T:C	F59L	0.836
X:71667980:C:A	F59L	0.836
X:71667980:C:G	F59L	0.836
X:71670655:T:C	L505P	0.823
X:71670612:T:A	C491S	0.810
X:71670613:G:C	C491S	0.810
X:71670614:C:G	C491W	0.808
X:71670612:T:C	C491R	0.802
X:71671218:T:C	F510L	0.800
X:71671220:C:A	F510L	0.800
X:71671220:C:G	F510L	0.800
X:71670326:T:A	C488S	0.793
X:71670327:G:C	C488S	0.793
X:71670652:A:C	Q504P	0.792
X:71671209:G:C	A507P	0.788
X:71671232:G:C	K514N	0.771
X:71671232:G:T	K514N	0.771
X:71670328:T:G	C488W	0.747
X:71670622:T:C	L494P	0.746
X:71671214:G:A	M508I	0.728
X:71671214:G:C	M508I	0.728
X:71671214:G:T	M508I	0.728

dbSNP variants (sampled 300 via entrez): RS1000180715 (X:71665671 G>A), RS1000473143 (X:71667955 G>A,T), RS1001457230 (X:71670034 A>G), RS1002235694 (X:71669278 A>C,G), RS1002266984 (X:71669523 C>T), RS1002346952 (X:71668788 C>G,T), RS1003271849 (X:71671023 A>G), RS1003448188 (X:71665922 C>G,T), RS1003463451 (X:71667473 C>A,T), RS1003757542 (X:71667609 G>A,C), RS1003826309 (X:71665583 G>T), RS1004139739 (X:71667423 C>T), RS1004588223 (X:71668739 C>T), RS1004870454 (X:71670839 G>A,T), RS1006002538 (X:71669881 G>A)

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: 0 entries

Clinical trials (associated diseases)

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