CCER2

Summary

CCER2 (coiled-coil glutamate rich protein 2, HGNC:44662) is a protein-coding gene on chromosome 19q13.2, encoding Coiled-coil domain-containing glutamate-rich protein 2 (I3L3R5).

Predicted to be located in extracellular region.

Source: NCBI Gene 643669 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 39 total
• MANE Select transcript: NM_001243212

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:44662
Approved symbol	CCER2
Name	coiled-coil glutamate rich protein 2
Location	19q13.2
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000262484
Ensembl biotype	protein_coding
OMIM	617634
Entrez	643669

Gene structure

Transcript identifiers

Ensembl transcripts: 2 — 2 protein_coding

ENST00000571838, ENST00000571845

RefSeq mRNA: 1 — MANE Select: NM_001243212 NM_001243212

CCDS: CCDS58661

Canonical transcript exons

ENST00000571838 — 5 exons

Exon	Start	End
ENSE00002637154	38912098	38912186
ENSE00002644802	38911566	38911653
ENSE00002650346	38908980	38909325
ENSE00002656607	38910563	38911083
ENSE00002680341	38911812	38911852

Expression profiles

Bgee: expression breadth ubiquitous, 128 present calls, max score 85.01.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 1.7019 / max 2038.1160, expressed in 49 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
180830	1.7019	49

Top tissues by expression

132 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	85.01	gold quality
ganglionic eminence	UBERON:0004023	78.82	gold quality
primary visual cortex	UBERON:0002436	76.77	gold quality
putamen	UBERON:0001874	73.92	gold quality
cerebellar hemisphere	UBERON:0002245	73.09	gold quality
cerebellar cortex	UBERON:0002129	73.07	gold quality
cerebellum	UBERON:0002037	73.02	gold quality
right hemisphere of cerebellum	UBERON:0014890	72.89	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	72.46	gold quality
caudate nucleus	UBERON:0001873	71.67	gold quality
right frontal lobe	UBERON:0002810	71.54	gold quality
nucleus accumbens	UBERON:0001882	71.05	gold quality
Ammon’s horn	UBERON:0001954	69.97	gold quality
superior frontal gyrus	UBERON:0002661	69.79	gold quality
anterior cingulate cortex	UBERON:0009835	69.72	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	69.60	gold quality
brain	UBERON:0000955	69.58	gold quality
temporal lobe	UBERON:0001871	69.48	gold quality
amygdala	UBERON:0001876	69.44	gold quality
skin of abdomen	UBERON:0001416	69.39	gold quality
zone of skin	UBERON:0000014	69.30	gold quality
skin of leg	UBERON:0001511	69.16	gold quality
gastrocnemius	UBERON:0001388	69.15	gold quality
substantia nigra	UBERON:0002038	68.62	gold quality
cerebral cortex	UBERON:0000956	68.47	gold quality
muscle of leg	UBERON:0001383	68.40	gold quality
right lobe of liver	UBERON:0001114	68.38	gold quality
hypothalamus	UBERON:0001898	68.25	gold quality
Brodmann (1909) area 9	UBERON:0013540	68.25	gold quality
right uterine tube	UBERON:0001302	67.81	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	0.57

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

14 targeting CCER2, 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-4455	100.00	65.48	1587
HSA-MIR-6740-5P	100.00	65.64	932
HSA-MIR-218-5P	99.93	72.22	2103
HSA-MIR-636	99.80	69.58	1500
HSA-MIR-1249-5P	99.61	66.55	2049
HSA-MIR-6797-5P	99.61	66.55	2084
HSA-MIR-12123	99.52	71.79	2990
HSA-MIR-504-3P	99.30	67.18	1745
HSA-MIR-4651	99.06	67.57	2002
HSA-MIR-4664-5P	98.17	65.07	1020
HSA-MIR-4443	98.02	66.25	1928
HSA-MIR-342-5P	97.25	64.10	817
HSA-MIR-1306-5P	97.11	64.04	755
HSA-MIR-3189-3P	96.80	66.34	896

Literature-anchored findings (GeneRIF, showing 1)

• the present study identified CCER2 as a novel susceptibility gene for MMD. CCER2 shows a brain-specific expression pattern, and its product has the structure of secreted proteins. (PMID:27717682)

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Ccer2	ENSMUSG00000096257
rattus_norvegicus	Ccer2	ENSRNOG00000046971

Protein

Protein identifiers

Coiled-coil domain-containing glutamate-rich protein 2 — I3L3R5 (reviewed: I3L3R5)

All UniProt accessions (2): I3L3R5, I3L3Z9

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Secreted.

Tissue specificity. Expressed at higher levels in fetal brain and skeletal muscle. Lower expression is detected in fetal kidney, liver, spleen, thymus, heart and lung.

RefSeq proteins (1): NP_001230141* (*=MANE)

Domains & families (InterPro)

UniProt features (21 total): sequence variant 14, compositionally biased region 4, signal peptide 1, chain 1, region of interest 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-I3L3R5-F1	70.74	0.22

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 11 (showing top): NFKBIA_TARGET_GENES, MIR218_5P, MIR4664_5P, MIR342_5P, BLANCO_MELO_HUMAN_PARAINFLUENZA_VIRUS_3_INFECTION_A594_CELLS_DN, BLANCO_MELO_RESPIRATORY_SYNCYTIAL_VIRUS_INFECTION_A594_CELLS_DN, MEBARKI_HCC_PROGENITOR_FZD8CRD_DN, DESCARTES_FETAL_CEREBRUM_MEGAKARYOCYTES, DESCARTES_FETAL_HEART_SATB2_LRRC7_POSITIVE_CELLS, DESCARTES_FETAL_MUSCLE_SATELLITE_CELLS, chr19q13

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (1): extracellular region (GO:0005576)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	1

Protein interactions and networks

STRING

156 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CCER2	CD164L2	Q6UWJ8	543
CCER2	RINL	Q6ZS11	487
CCER2	RNF213	Q63HN8	439
CCER2	STK32A	Q8WU08	433
CCER2	ACBD7	Q8N6N7	418
CCER2	CLMB	Q96GX8	417
CCER2	ST8SIA3	O43173	408
CCER2	EMID1	Q96A84	405
CCER2	PPM1L	Q5SGD2	399
CCER2	SAP25	Q8TEE9	397
CCER2	PRND	Q9UKY0	365
CCER2	SLC52A3	Q9NQ40	364
CCER2	HYDIN	Q4G0P3	360
CCER2	HSF5	Q4G112	357
CCER2	MYO3A	Q8NEV4	357

IntAct

0 interactions, top by confidence:

ESM2 similar proteins: A5LHG2, B0VXV8, B8K1V9, C6EVG7, D5J9S0, D9IX97, D9IX98, F5CPE8, I3L3R5, O46540, P01021, P07480, P09681, P09876, P09916, P0C7P5, P0C7P6, P0DMD5, P11242, P13085, P13205, P16860, P22858, P23943, P40753, P41547, P43026, P43027, P56469, P68515, P70160, P79799, P83228, P87385, Q06145, Q1RMJ9, Q27J49, Q2XXL8, Q60478, Q62949

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	13
Likely benign	15
Benign	11

Top pathogenic / likely-pathogenic (0)

SpliceAI

619 predictions. Top by Δscore:

Variant	Effect	Δscore
19:38911079:CAACT:C	acceptor_gain	1.0000
19:38911082:CT:C	acceptor_gain	1.0000
19:38911083:TCTGG:T	acceptor_loss	0.9900
19:38911084:C:CC	acceptor_gain	0.9900
19:38911084:C:CG	acceptor_loss	0.9900
19:38911085:T:A	acceptor_loss	0.9900
19:38911089:A:T	acceptor_gain	0.9900
19:38911564:AC:A	donor_gain	0.9900
19:38911565:CC:C	donor_gain	0.9900
19:38911651:CAG:C	acceptor_gain	0.9900
19:38911654:C:CC	acceptor_gain	0.9900
19:38911813:T:TA	donor_gain	0.9900
19:38911850:TGG:T	acceptor_gain	0.9900
19:38911853:C:CC	acceptor_gain	0.9900
19:38912095:CACCC:C	donor_loss	0.9900
19:38912096:AC:A	donor_gain	0.9900
19:38912096:ACCCG:A	donor_gain	0.9900
19:38912097:C:CT	donor_loss	0.9900
19:38912097:CC:C	donor_gain	0.9900
19:38912097:CCCG:C	donor_gain	0.9900
19:38912097:CCCGC:C	donor_gain	0.9900
19:38911080:AACT:A	acceptor_gain	0.9800
19:38911088:C:CT	acceptor_gain	0.9800
19:38911652:AG:A	acceptor_gain	0.9800
19:38911652:AGCTG:A	acceptor_loss	0.9800
19:38911653:GCT:G	acceptor_loss	0.9800
19:38911654:CTGGG:C	acceptor_loss	0.9800
19:38911655:T:C	acceptor_loss	0.9800
19:38911849:GTGG:G	acceptor_gain	0.9800
19:38911849:GTGGC:G	acceptor_loss	0.9800

AlphaMissense

1733 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
19:38909285:A:G	L251P	0.904
19:38910731:G:C	F181L	0.904
19:38910731:G:T	F181L	0.904
19:38910733:A:G	F181L	0.904
19:38911644:A:G	C38R	0.887
19:38911628:A:T	V43D	0.872
19:38910680:C:A	W198C	0.855
19:38910680:C:G	W198C	0.855
19:38911642:A:C	C38W	0.851
19:38911587:A:G	C57R	0.849
19:38911643:C:G	C38S	0.844
19:38911644:A:T	C38S	0.844
19:38911585:G:C	C57W	0.842
19:38911586:C:T	C57Y	0.833
19:38911818:C:A	K32N	0.807
19:38911818:C:G	K32N	0.807
19:38911607:C:A	G50V	0.806
19:38911586:C:G	C57S	0.805
19:38911587:A:T	C57S	0.805
19:38909281:C:A	K252N	0.798
19:38909281:C:G	K252N	0.798
19:38911640:A:G	L39P	0.797
19:38911643:C:T	C38Y	0.788
19:38911638:C:G	A40P	0.779
19:38909273:G:A	T255I	0.775
19:38910809:C:A	W155C	0.774
19:38910809:C:G	W155C	0.774
19:38911616:A:G	L47P	0.773
19:38911574:A:T	L61H	0.770
19:38911016:G:C	F86L	0.742

dbSNP variants (sampled 300 via entrez): RS1001070695 (19:38912931 T>C), RS1001189911 (19:38909573 C>G,T), RS1001572692 (19:38910094 A>C,G), RS1002739175 (19:38909295 T>C), RS1002861866 (19:38910670 C>T), RS1003230899 (19:38912677 G>A), RS1004110034 (19:38910498 C>T), RS1004542286 (19:38910655 C>T), RS1004685655 (19:38910074 T>C), RS1005555607 (19:38913362 A>G), RS1005812269 (19:38911643 C>T), RS1006148141 (19:38909053 CAG>C), RS1006195566 (19:38911355 C>G), RS1006956262 (19:38912742 C>T), RS1007030167 (19:38913030 T>C)

Disease associations

OMIM: gene MIM:617634 | 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)

PharmGKB variants

1 variants.

Variant	Genes	Level	Score	#Clin annots	Drugs
rs3136646	CCER2, NFKBIB		0.00	0

CTD chemical–gene interactions

5 total (human), top 5 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
butyraldehyde	decreases expression	1
jinfukang	affects cotreatment, decreases expression	1
Benzo(a)pyrene	decreases expression	1
Cisplatin	affects cotreatment, decreases expression	1
Tobacco Smoke Pollution	decreases expression	1

Clinical trials (associated diseases)

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