CCSER2

Summary

CCSER2 (coiled-coil serine rich protein 2, HGNC:29197) is a protein-coding gene on chromosome 10q23.1, encoding Serine-rich coiled-coil domain-containing protein 2 (Q9H7U1). Microtubule-binding protein which might play a role in microtubule bundling.

Predicted to enable microtubule binding activity. Predicted to be involved in microtubule bundle formation. Predicted to be located in cytoplasm and cytoskeleton. Predicted to be active in microtubule cytoskeleton.

Source: NCBI Gene 54462 — RefSeq curated summary.

At a glance

• GWAS associations: 4
• Clinical variants (ClinVar): 154 total
• MANE Select transcript: NM_001284240

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:29197
Approved symbol	CCSER2
Name	coiled-coil serine rich protein 2
Location	10q23.1
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000107771
Ensembl biotype	protein_coding
OMIM	619944
Entrez	54462

Gene structure

Transcript identifiers

Ensembl transcripts: 13 — 10 protein_coding, 2 protein_coding_CDS_not_defined, 1 nonsense_mediated_decay

ENST00000224756, ENST00000359979, ENST00000372088, ENST00000466105, ENST00000480006, ENST00000493409, ENST00000494144, ENST00000494586, ENST00000498300, ENST00000543283, ENST00000898573, ENST00000917261, ENST00000945736

RefSeq mRNA: 7 — MANE Select: NM_001284240 NM_001284240, NM_001284241, NM_001284242, NM_001284243, NM_001351290, NM_001351292, NM_018999

CCDS: CCDS31235, CCDS60582, CCDS60583, CCDS73159

Canonical transcript exons

ENST00000372088 — 10 exons

Exon	Start	End
ENSE00001623563	84513449	84518517
ENSE00001687607	84373619	84373815
ENSE00001795795	84371014	84372469
ENSE00003504980	84463933	84464016
ENSE00003525739	84417771	84417861
ENSE00003565300	84425731	84425893
ENSE00003592576	84470372	84470458
ENSE00003607136	84438512	84438707
ENSE00003639567	84477575	84477664
ENSE00003714645	84328589	84328808

Expression profiles

Bgee: expression breadth ubiquitous, 291 present calls, max score 99.73.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 28.6233 / max 542.7415, expressed in 1779 samples.

FANTOM5 promoters (10 alternative TSS)

Promoter ID	TPM avg	Samples expressed
105942	15.2019	1742
105941	5.3330	1573
105950	4.7568	992
105940	1.9800	955
105953	0.6241	78
105948	0.2373	57
105951	0.2171	125
105952	0.1775	50
105949	0.0542	3
105954	0.0415	23

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
sperm	CL:0000019	99.73	gold quality
male germ cell	CL:0000015	99.05	gold quality
dorsal root ganglion	UBERON:0000044	97.83	gold quality
left testis	UBERON:0004533	97.56	gold quality
right testis	UBERON:0004534	97.39	gold quality
endothelial cell	CL:0000115	97.13	gold quality
trigeminal ganglion	UBERON:0001675	96.73	gold quality
testis	UBERON:0000473	96.17	gold quality
calcaneal tendon	UBERON:0003701	96.12	gold quality
Brodmann (1909) area 23	UBERON:0013554	95.14	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	95.13	gold quality
pons	UBERON:0000988	94.95	gold quality
colonic epithelium	UBERON:0000397	94.88	gold quality
corpus callosum	UBERON:0002336	94.35	gold quality
skeletal muscle tissue of biceps brachii	UBERON:0004502	94.09	gold quality
biceps brachii	UBERON:0001507	94.03	gold quality
superior vestibular nucleus	UBERON:0007227	93.62	gold quality
tibialis anterior	UBERON:0001385	93.50	gold quality
vastus lateralis	UBERON:0001379	93.46	gold quality
quadriceps femoris	UBERON:0001377	93.17	gold quality
deltoid	UBERON:0001476	93.13	gold quality
tendon	UBERON:0000043	92.90	gold quality
saphenous vein	UBERON:0007318	92.88	gold quality
skeletal muscle organ	UBERON:0014892	92.76	gold quality
muscle organ	UBERON:0001630	92.75	gold quality
cerebellar vermis	UBERON:0004720	92.74	gold quality
muscle of leg	UBERON:0001383	92.67	gold quality
skeletal muscle tissue	UBERON:0001134	92.55	gold quality
adrenal tissue	UBERON:0018303	92.52	gold quality
superior frontal gyrus	UBERON:0002661	92.47	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-GEOD-134144	yes	32.05
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

294 targeting CCSER2, 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-6867-5P	100.00	82.21	3464
HSA-MIR-1277-5P	100.00	73.95	5056
HSA-MIR-9-5P	100.00	72.28	2361
HSA-MIR-513A-5P	100.00	69.77	2465
HSA-MIR-5011-5P	100.00	83.46	5820
HSA-MIR-29A-3P	100.00	73.11	1835
HSA-MIR-29B-3P	100.00	73.18	1833
HSA-MIR-29C-3P	100.00	73.15	1833
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-656-3P	100.00	72.15	2788
HSA-MIR-5692A	100.00	74.40	6850
HSA-MIR-450A-1-3P	100.00	69.33	1837
HSA-MIR-4747-5P	100.00	67.90	2681
HSA-MIR-5196-5P	100.00	67.98	2761
HSA-MIR-4262	100.00	73.26	3931
HSA-MIR-190A-3P	100.00	80.35	5520
HSA-MIR-7110-3P	100.00	73.18	2486
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-1252-5P	100.00	69.80	2774
HSA-MIR-371B-5P	99.99	75.34	4759
HSA-MIR-3662	99.99	73.82	5684
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-6870-5P	99.99	68.55	2115
HSA-MIR-4282	99.99	75.36	6408
HSA-MIR-4775	99.98	75.00	6394
HSA-MIR-5696	99.98	72.36	4487
HSA-MIR-8068	99.98	73.85	2376
HSA-MIR-19A-3P	99.98	75.33	2762
HSA-MIR-19B-3P	99.98	75.44	2754
HSA-MIR-373-5P	99.98	75.36	4753

Literature-anchored findings (GeneRIF, showing 1)

• Characterization of human Ccser2 as a protein tracking the plus-ends of microtubules. (PMID:37684684)

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	ccser2a	ENSDARG00000087749
danio_rerio	ccser2b	ENSDARG00000091535
mus_musculus	Ccser2	ENSMUSG00000058690
rattus_norvegicus	Ccser2	ENSRNOG00000022781

Paralogs (1): CCSER1 (ENSG00000184305)

Protein

Protein identifiers

Serine-rich coiled-coil domain-containing protein 2 — Q9H7U1 (reviewed: Q9H7U1)

Alternative names: Coiled-coil serine-rich protein 2, Protein GCAP14 homolog

All UniProt accessions (5): Q9H7U1, A0A2R8Y6V5, A0A2R8Y7M2, A0A2R8YGE2, A0A2R8YGU6

UniProt curated annotations — full annotation on UniProt →

Function. Microtubule-binding protein which might play a role in microtubule bundling.

Subcellular location. Cytoplasm. Cytoskeleton.

Similarity. Belongs to the CCSER family.

Isoforms (4)

UniProt ID	Names	Canonical?
Q9H7U1-1	1	yes
Q9H7U1-2	2
Q9H7U1-3	3
Q9H7U1-4	4

RefSeq proteins (7): NP_001271169, NP_001271170, NP_001271171, NP_001271172, NP_001338219, NP_001338221, NP_061872 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR029627	CCSER	Family

UniProt features (33 total): sequence conflict 8, compositionally biased region 7, region of interest 6, splice variant 4, sequence variant 4, modified residue 2, chain 1, coiled-coil region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9H7U1-F1	48.62	0.06

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Post-translational modifications (2): 223, 452

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 225 (showing top): TGGTGCT_MIR29A_MIR29B_MIR29C, YAATNRNNNYNATT_UNKNOWN, GRAESSMANN_APOPTOSIS_BY_SERUM_DEPRIVATION_UP, TGACCTY_ERR1_Q2, CTATGCA_MIR153, NKX61_01, DEURIG_T_CELL_PROLYMPHOCYTIC_LEUKEMIA_DN, RUTELLA_RESPONSE_TO_CSF2RB_AND_IL4_UP, RUTELLA_RESPONSE_TO_HGF_VS_CSF2RB_AND_IL4_DN, DACOSTA_UV_RESPONSE_VIA_ERCC3_COMMON_DN, GENTILE_UV_RESPONSE_CLUSTER_D9, TGACATY_UNKNOWN, GOBP_MICROTUBULE_BUNDLE_FORMATION, GATA1_04, AACTTT_UNKNOWN

GO Biological Process (1): microtubule bundle formation (GO:0001578)

GO Molecular Function (2): microtubule binding (GO:0008017), protein binding (GO:0005515)

GO Cellular Component (3): microtubule cytoskeleton (GO:0015630), cytoplasm (GO:0005737), cytoskeleton (GO:0005856)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
microtubule cytoskeleton organization	1
tubulin binding	1
binding	1
cytoskeleton	1
intracellular anatomical structure	1
cellular anatomical structure	1
intracellular membraneless organelle	1

Protein interactions and networks

STRING

492 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CCSER2	DYDC1	Q8WWB3	555
CCSER2	NDEL1	Q9GZM8	529
CCSER2	NDE1	Q9NXR1	514
CCSER2	SYNE1	Q8NF91	486
CCSER2	DYDC2	Q96IM9	483
CCSER2	TSPAN14	Q8NG11	457
CCSER2	SYMPK	Q92797	444
CCSER2	PUM1	Q14671	441
CCSER2	ANKRD17	O75179	418
CCSER2	MATCAP2	Q8NCT3	412
CCSER2	LUZP1	Q86V48	409
CCSER2	B8ZZ87	B8ZZ87	408
CCSER2	FAM117B	Q6P1L5	408
CCSER2	GHITM	Q9H3K2	402
CCSER2	PRR20A	P86496	398

IntAct

62 interactions, top by confidence:

A	B	Type	Score
YWHAB	PIK3C2A	psi-mi:“MI:0914”(association)	0.800
BRK1	HSBP1	psi-mi:“MI:0914”(association)	0.740
DYNLL1	BLTP3B	psi-mi:“MI:0914”(association)	0.730
SLMAP	STRN	psi-mi:“MI:2364”(proximity)	0.710
YWHAG	BLTP3B	psi-mi:“MI:0914”(association)	0.640
DYNLL2	BLTP3B	psi-mi:“MI:0914”(association)	0.640
YWHAH	PLEKHG3	psi-mi:“MI:0914”(association)	0.610
YWHAE	PIK3C2A	psi-mi:“MI:0914”(association)	0.570
YWHAH	BLTP3B	psi-mi:“MI:0914”(association)	0.570
YWHAG	SHTN1	psi-mi:“MI:0914”(association)	0.560
YWHAQ	IGLC7	psi-mi:“MI:0914”(association)	0.530
NDEL1	OFD1	psi-mi:“MI:0914”(association)	0.530
PNMA2	CCDC85C	psi-mi:“MI:0914”(association)	0.530
CCSER2	NES	psi-mi:“MI:0915”(physical association)	0.400
Nde1	RPA2	psi-mi:“MI:0915”(physical association)	0.400
MAP1LC3B	CCSER2	psi-mi:“MI:0915”(physical association)	0.370
Pafah1b1	ATXN3	psi-mi:“MI:0914”(association)	0.350
EGLN3	FAM168B	psi-mi:“MI:0914”(association)	0.350
YWHAG	C1orf226	psi-mi:“MI:0914”(association)	0.350
DYRK2	ZSWIM8	psi-mi:“MI:0914”(association)	0.350
YWHAH	SHTN1	psi-mi:“MI:0914”(association)	0.350
YWHAQ	MCRIP1	psi-mi:“MI:0914”(association)	0.350
MAPRE1	SCAMP1	psi-mi:“MI:0914”(association)	0.350
PICALM	RPN1	psi-mi:“MI:0914”(association)	0.350

BioGRID (91): CCSER2 (Proximity Label-MS), CCSER2 (Proximity Label-MS), CCSER2 (Affinity Capture-MS), CCSER2 (Affinity Capture-MS), CCSER2 (Affinity Capture-MS), CCSER2 (Proximity Label-MS), CCSER2 (Affinity Capture-MS), CCSER2 (Affinity Capture-MS), CCSER2 (Two-hybrid), CCSER2 (Affinity Capture-MS), CCSER2 (Proximity Label-MS), CCSER2 (Affinity Capture-RNA), CCSER2 (Two-hybrid), CCSER2 (Two-hybrid), CCSER2 (Two-hybrid)

ESM2 similar proteins: A1YF19, A2T767, B0K035, F1RCE7, F7BHS0, O95997, P0DPK0, P23999, P97613, Q08B36, Q08BD8, Q09HN1, Q0VA20, Q14140, Q2KHM9, Q2QD14, Q2QD15, Q2T9X8, Q2WG80, Q3SZY3, Q3UHI0, Q3V1H1, Q5R7F8, Q5RBY6, Q5RKG1, Q5XG16, Q5ZJU5, Q6A000, Q6AYH4, Q6DF94, Q7SXC6, Q8BHE0, Q8BHZ5, Q8C804, Q8N0Z3, Q8QGU6, Q8R080, Q8WWK9, Q96C57, Q96FF9

Diamond homologs: Q1RMS0, Q3UHI0, Q8C0C4, Q9C0I3, Q9H7U1

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 59 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

Pathway	Partners	Fold	FDR
Activation of BAD and translocation to mitochondria	7	118.4×	1e-11
Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex	7	104.5×	2e-11
SARS-CoV-1 targets host intracellular signalling and regulatory pathways	7	104.5×	2e-11
Activation of BH3-only proteins	7	77.2×	2e-10
RHO GTPases activate PKNs	7	49.4×	3e-09
Intrinsic Pathway for Apoptosis	7	45.5×	6e-09
FOXO-mediated transcription	6	44.8×	7e-08
Apoptosis	8	29.9×	8e-09

GO biological processes:

GO term	Partners	Fold	FDR
protein targeting	6	41.5×	1e-06
substantia nigra development	5	34.6×	5e-05
intracellular protein localization	10	19.8×	3e-08
endocytosis	6	10.8×	2e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	133
Likely benign	7
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

3082 predictions. Top by Δscore:

Variant	Effect	Δscore
10:84372457:A:G	donor_gain	1.0000
10:84373811:GCATA:G	donor_gain	1.0000
10:84373812:CATA:C	donor_gain	1.0000
10:84373814:TA:T	donor_gain	1.0000
10:84373816:G:GG	donor_gain	1.0000
10:84417765:TCACA:T	acceptor_loss	1.0000
10:84417766:CACAG:C	acceptor_loss	1.0000
10:84417768:CAGGA:C	acceptor_loss	1.0000
10:84417769:A:AG	acceptor_gain	1.0000
10:84417769:AG:A	acceptor_gain	1.0000
10:84417769:AGGAT:A	acceptor_loss	1.0000
10:84417770:G:A	acceptor_loss	1.0000
10:84417770:G:GG	acceptor_gain	1.0000
10:84417770:GG:G	acceptor_gain	1.0000
10:84417770:GGAT:G	acceptor_gain	1.0000
10:84417860:TG:T	donor_gain	1.0000
10:84417861:GG:G	donor_gain	1.0000
10:84417862:G:GC	donor_loss	1.0000
10:84417863:T:G	donor_loss	1.0000
10:84425729:A:AG	acceptor_gain	1.0000
10:84425729:AGT:A	acceptor_gain	1.0000
10:84425729:AGTG:A	acceptor_gain	1.0000
10:84425730:G:GG	acceptor_gain	1.0000
10:84425730:GT:G	acceptor_gain	1.0000
10:84425730:GTG:G	acceptor_gain	1.0000
10:84425730:GTGG:G	acceptor_gain	1.0000
10:84425730:GTGGA:G	acceptor_gain	1.0000
10:84425890:GCAG:G	donor_gain	1.0000
10:84425891:CAGG:C	donor_loss	1.0000
10:84425892:AGGT:A	donor_loss	1.0000

AlphaMissense

6964 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
10:84373738:T:A	W513R	1.000
10:84373738:T:C	W513R	1.000
10:84373740:G:C	W513C	0.999
10:84373740:G:T	W513C	0.999
10:84438688:T:C	L682P	0.999
10:84373717:A:C	S506R	0.998
10:84373719:C:A	S506R	0.998
10:84373719:C:G	S506R	0.998
10:84470403:T:C	L727P	0.998
10:84417817:T:C	L554P	0.997
10:84417823:T:C	L556P	0.997
10:84438657:T:C	C672R	0.997
10:84438679:T:C	L679S	0.997
10:84373739:G:C	W513S	0.996
10:84373741:G:C	D514H	0.996
10:84373742:A:T	D514V	0.995
10:84417778:T:C	L541S	0.995
10:84417823:T:A	L556H	0.995
10:84438637:T:C	L665P	0.995
10:84438659:C:G	C672W	0.995
10:84438682:T:C	L680P	0.995
10:84373732:T:G	Y511D	0.994
10:84373742:A:C	D514A	0.994
10:84373810:A:C	S537R	0.994
10:84373812:C:A	S537R	0.994
10:84373812:C:G	S537R	0.994
10:84371719:A:C	S223R	0.993
10:84371721:T:A	S223R	0.993
10:84371721:T:G	S223R	0.993
10:84373703:T:C	L501P	0.993

dbSNP variants (sampled 300 via entrez): RS1000001388 (10:84447892 G>A), RS1000008943 (10:84427706 C>G,T), RS1000032662 (10:84343724 A>G), RS1000044661 (10:84516328 C>A,G), RS1000055821 (10:84426443 G>T), RS1000065559 (10:84434378 T>C), RS1000066216 (10:84384107 A>G), RS1000099549 (10:84461002 G>A), RS1000103416 (10:84427934 C>T), RS1000115530 (10:84483087 A>G), RS1000142215 (10:84370871 G>A,C,T), RS1000147017 (10:84504203 C>T), RS1000148891 (10:84362271 G>A), RS1000163320 (10:84438241 T>C), RS1000185070 (10:84338298 A>C)

Disease associations

OMIM: gene MIM:619944 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

4 associations (top):

Study	Trait	p-value
GCST004070_20	Cerebrospinal P-tau181p levels	5.000000e-06
GCST005351_3	Carboplatin disposition in epthelial ovarian cancer	7.000000e-06
GCST009144_3	Disease progression in age-related macular degeneration (adjusted for baseline)	3.000000e-06
GCST010002_293	Refractive error	1.000000e-70

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0004763	p-tau measurement
EFO:0008336	disease progression measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Acetaminophen	increases expression	2
Valproic Acid	increases expression, increases methylation	2
Cyclosporine	increases expression	2
aristolochic acid I	decreases expression	1
GSK-J4	increases expression	1
triphenyl phosphate	affects expression	1
arsenite	increases reaction, affects binding	1
tris(1,3-dichloro-2-propyl)phosphate	increases expression	1
sodium arsenite	increases expression	1
cobaltous chloride	increases expression	1
butyraldehyde	decreases expression	1
potassium chromate(VI)	affects cotreatment, decreases expression	1
epigallocatechin gallate	affects cotreatment, decreases expression	1
di-n-butylphosphoric acid	affects expression	1
K 7174	increases expression	1
torcetrapib	increases expression	1
abrine	increases expression	1
PCI 5002	affects cotreatment, increases expression	1
Temozolomide	decreases expression	1
Sunitinib	increases expression	1
Leflunomide	increases expression	1
Vehicle Emissions	increases abundance, decreases expression	1
Benzo(a)pyrene	increases methylation	1
Cadmium	decreases expression, increases abundance	1
Caffeine	increases phosphorylation	1
Dichlorodiphenyl Dichloroethylene	decreases expression	1
Dimethyl Sulfoxide	increases expression	1
Doxorubicin	decreases expression	1
Hydrogen Peroxide	affects cotreatment, increases expression	1
Lead	affects splicing	1

Clinical trials (associated diseases)

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