CLBA1

Summary

CLBA1 (clathrin binding box of aftiphilin containing 1, HGNC:20126) is a protein-coding gene on chromosome 14q32.33, encoding Uncharacterized protein CLBA1 (Q96F83).

Predicted to enable clathrin binding activity. Predicted to be involved in intracellular transport. Predicted to be part of AP-1 adaptor complex. Predicted to be active in trans-Golgi network membrane.

Source: NCBI Gene 122616 — RefSeq curated summary.

At a glance

• GWAS associations: 2
• Clinical variants (ClinVar): 11 total
• MANE Select transcript: NM_174891

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:20126
Approved symbol	CLBA1
Name	clathrin binding box of aftiphilin containing 1
Location	14q32.33
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000140104
Ensembl biotype	protein_coding
Entrez	122616

Gene structure

Transcript identifiers

Ensembl transcripts: 9 — 4 protein_coding, 2 nonsense_mediated_decay, 2 protein_coding_CDS_not_defined, 1 retained_intron

ENST00000389964, ENST00000547315, ENST00000548178, ENST00000548641, ENST00000549240, ENST00000549584, ENST00000550614, ENST00000551046, ENST00000551606

RefSeq mRNA: 2 — MANE Select: NM_174891 NM_001364170, NM_174891

CCDS: CCDS42000

Canonical transcript exons

ENST00000547315 — 5 exons

Exon	Start	End
ENSE00002419749	104985788	104986854
ENSE00002428902	104994598	104995516
ENSE00003504039	104988943	104989088
ENSE00003504731	104991491	104991620
ENSE00003516447	104992948	104993064

Expression profiles

Bgee: expression breadth ubiquitous, 191 present calls, max score 95.33.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 3.6935 / max 32.4781, expressed in 1457 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
141860	3.6935	1457

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
right uterine tube	UBERON:0001302	95.33	gold quality
right testis	UBERON:0004534	90.84	gold quality
left testis	UBERON:0004533	90.47	gold quality
adenohypophysis	UBERON:0002196	88.26	gold quality
right lobe of thyroid gland	UBERON:0001119	87.62	gold quality
testis	UBERON:0000473	87.28	gold quality
pituitary gland	UBERON:0000007	86.77	gold quality
left lobe of thyroid gland	UBERON:0001120	86.63	gold quality
bronchial epithelial cell	CL:0002328	86.34	gold quality
metanephros cortex	UBERON:0010533	86.04	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	85.89	gold quality
thyroid gland	UBERON:0002046	85.66	gold quality
parotid gland	UBERON:0001831	85.49	silver quality
olfactory segment of nasal mucosa	UBERON:0005386	85.48	gold quality
epithelium of bronchus	UBERON:0002031	85.20	gold quality
bronchus	UBERON:0002185	84.47	gold quality
body of pancreas	UBERON:0001150	83.68	gold quality
prefrontal cortex	UBERON:0000451	81.80	gold quality
right frontal lobe	UBERON:0002810	81.62	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	81.45	gold quality
pancreas	UBERON:0001264	81.04	gold quality
right adrenal gland	UBERON:0001233	80.87	gold quality
right adrenal gland cortex	UBERON:0035827	80.61	gold quality
nucleus accumbens	UBERON:0001882	80.05	gold quality
islet of Langerhans	UBERON:0000006	79.98	gold quality
cortical plate	UBERON:0005343	79.78	gold quality
left adrenal gland cortex	UBERON:0035825	79.71	gold quality
left adrenal gland	UBERON:0001234	79.70	gold quality
ventricular zone	UBERON:0003053	79.35	gold quality
cingulate cortex	UBERON:0003027	79.31	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	4.74

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

18 targeting CLBA1, 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-4306	99.72	70.50	3630
HSA-MIR-548M	99.70	68.87	1749
HSA-MIR-1324	99.46	66.57	1302
HSA-MIR-542-3P	99.34	67.58	1270
HSA-MIR-6505-3P	99.34	67.39	1071
HSA-MIR-12113	99.32	67.54	1072
HSA-MIR-670-3P	99.03	68.88	2404
HSA-MIR-6876-3P	98.97	65.69	765
HSA-MIR-626	98.89	66.21	762
HSA-MIR-760	98.81	66.65	1392
HSA-MIR-4539	98.78	67.18	888
HSA-MIR-6840-3P	98.68	65.95	1923
HSA-MIR-6764-3P	98.44	67.64	1153
HSA-MIR-6824-3P	98.44	67.62	1154
HSA-MIR-214-5P	97.34	66.50	617
HSA-MIR-6748-3P	97.20	65.66	836
HSA-MIR-3126-5P	96.87	65.83	912
HSA-MIR-6875-5P	96.87	65.49	958

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
mus_musculus	Clba1	ENSMUSG00000037594
rattus_norvegicus	Clba1	ENSRNOG00000013690
caenorhabditis_elegans		WBGENE00021561

Paralogs (1): AFTPH (ENSG00000119844)

Protein

Protein identifiers

Uncharacterized protein CLBA1 — Q96F83 (reviewed: Q96F83)

Alternative names: Clathrin-binding box of aftiphilin-containing protein 1

All UniProt accessions (5): Q96F83, F8VUA8, H0YHP6, J3KPM0, J3KRA4

RefSeq proteins (2): NP_001351099, NP_777551* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR029205	Clathrin-bd	Domain
IPR046359	Aftin-like	Family

Pfam: PF15045

UniProt features (4 total): region of interest 3, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q96F83-F1	50.43	0.00

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 84 (showing top): GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_UP, GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_UP, MONNIER_POSTRADIATION_TUMOR_ESCAPE_UP, GOCC_TRANS_GOLGI_NETWORK, GOCC_COATED_VESICLE, COATES_MACROPHAGE_M1_VS_M2_UP, GOCC_GOLGI_ASSOCIATED_VESICLE, GOCC_VESICLE_COAT, KUNINGER_IGF1_VS_PDGFB_TARGETS_DN, MORF_MT4, chr14q32, GOCC_CLATHRIN_COATED_VESICLE, GOCC_TRANS_GOLGI_NETWORK_TRANSPORT_VESICLE_MEMBRANE, GOCC_GOLGI_ASSOCIATED_VESICLE_MEMBRANE, GOCC_CLATHRIN_COAT

GO Biological Process (1): intracellular transport (GO:0046907)

GO Molecular Function (1): clathrin binding (GO:0030276)

GO Cellular Component (2): AP-1 adaptor complex (GO:0030121), trans-Golgi network membrane (GO:0032588)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
intracellular anatomical structure	1
transport	1
cellular localization	1
establishment of localization in cell	1
protein binding	1
clathrin coat of trans-Golgi network vesicle	1
clathrin adaptor complex	1
trans-Golgi network	1
organelle membrane	1

Protein interactions and networks

STRING

390 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CLBA1	VWA5B2	Q8N398	610
CLBA1	C2orf72	A6NCS6	583
CLBA1	KIF9	Q9HAQ2	557
CLBA1	ANKEF1	Q9NU02	554
CLBA1	LRWD1	Q9UFC0	541
CLBA1	OAZ3	Q9UMX2	523
CLBA1	LRATD2	Q96KN1	507
CLBA1	C1orf226	A1L170	506
CLBA1	RELT	Q969Z4	504
CLBA1	SPATA21	Q7Z572	490
CLBA1	TICRR	Q7Z2Z1	476
CLBA1	ZNF839	A8K0R7	472
CLBA1	ADCY7	P51828	457
CLBA1	FYB2	Q5VWT5	447
CLBA1	FAAP24	Q9BTP7	437

IntAct

2 interactions, top by confidence:

A	B	Type	Score
CLBA1	FAT3	psi-mi:“MI:0915”(physical association)	0.400

BioGRID (5): FAT3 (Affinity Capture-MS), C14orf79 (Affinity Capture-RNA), C14orf79 (Affinity Capture-MS), C14orf79 (Affinity Capture-MS), C14orf79 (Affinity Capture-RNA)

ESM2 similar proteins: A0A1B0GVZ6, A6H7B4, A6NFA0, A6NGY1, A6QP24, A9YTQ3, B2RQL2, D3ZUC4, D4AAA5, E9Q286, P0C1T1, P0C6A0, P50617, Q0KK55, Q15583, Q17QP7, Q1RN00, Q283Q6, Q3SYA9, Q3UN58, Q49AJ0, Q5BMD4, Q5DU28, Q5IS58, Q5M831, Q5RJN9, Q5ZK13, Q66H03, Q68DA7, Q68US1, Q6PAC4, Q76NI1, Q80TS7, Q80VY2, Q8BHN9, Q8BII1, Q8CGM2, Q8IY42, Q8K2F3, Q8NHZ7

Diamond homologs: Q17QP7, Q5RJN9, Q8BHN9, Q96F83, Q6ULP2

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	5
Likely benign	1
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

962 predictions. Top by Δscore:

Variant	Effect	Δscore
14:104988939:TCAG:T	acceptor_loss	1.0000
14:104988941:A:AG	acceptor_gain	1.0000
14:104988941:A:C	acceptor_loss	1.0000
14:104988942:G:A	acceptor_loss	1.0000
14:104988942:G:GA	acceptor_gain	1.0000
14:104988942:GC:G	acceptor_gain	1.0000
14:104988942:GCC:G	acceptor_gain	1.0000
14:104988942:GCCC:G	acceptor_gain	1.0000
14:104988942:GCCCA:G	acceptor_gain	1.0000
14:104989086:GTG:G	donor_gain	1.0000
14:104991487:CCA:C	acceptor_loss	1.0000
14:104991489:A:AG	acceptor_gain	1.0000
14:104991489:A:AT	acceptor_loss	1.0000
14:104991490:G:GA	acceptor_gain	1.0000
14:104991490:GT:G	acceptor_gain	1.0000
14:104991490:GTA:G	acceptor_gain	1.0000
14:104991490:GTAA:G	acceptor_gain	1.0000
14:104991490:GTAAC:G	acceptor_gain	1.0000
14:104991492:AAC:A	acceptor_gain	1.0000
14:104991616:AGAAG:A	donor_loss	1.0000
14:104991617:GAAG:G	donor_gain	1.0000
14:104991618:AAGGT:A	donor_loss	1.0000
14:104991619:AGG:A	donor_loss	1.0000
14:104991620:GGTAG:G	donor_loss	1.0000
14:104991621:GTA:G	donor_loss	1.0000
14:104991622:T:A	donor_loss	1.0000
14:104992944:TTA:T	acceptor_loss	1.0000
14:104992946:A:AG	acceptor_gain	1.0000
14:104992947:G:GA	acceptor_gain	1.0000
14:104992947:GA:G	acceptor_gain	1.0000

AlphaMissense

2130 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
14:104986672:T:C	F81L	0.980
14:104986674:T:A	F81L	0.980
14:104986674:T:G	F81L	0.980
14:104986681:T:C	F84L	0.978
14:104986683:T:A	F84L	0.978
14:104986683:T:G	F84L	0.978
14:104988979:T:C	F154L	0.974
14:104988981:T:A	F154L	0.974
14:104988981:T:G	F154L	0.974
14:104994649:T:C	F290L	0.948
14:104994651:C:A	F290L	0.948
14:104994651:C:G	F290L	0.948
14:104986663:T:A	W78R	0.946
14:104986663:T:C	W78R	0.946
14:104986665:G:C	W78C	0.943
14:104986665:G:T	W78C	0.943
14:104991601:G:T	G227V	0.920
14:104986682:T:C	F84S	0.918
14:104988980:T:C	F154S	0.917
14:104991512:G:C	W197C	0.916
14:104991512:G:T	W197C	0.916
14:104993054:T:C	I269T	0.912
14:104991510:T:A	W197R	0.900
14:104991510:T:C	W197R	0.900
14:104994709:T:C	F310L	0.899
14:104994711:C:A	F310L	0.899
14:104994711:C:G	F310L	0.899
14:104986673:T:G	F81C	0.894
14:104994739:T:C	F320L	0.893
14:104994741:T:A	F320L	0.893

dbSNP variants (sampled 300 via entrez): RS1000277734 (14:104998196 C>T), RS1000469163 (14:104984134 G>A), RS1000834875 (14:104993942 CAGG>C), RS1000970133 (14:104994173 C>G,T), RS1001040374 (14:104988846 C>A), RS1001297170 (14:104992737 G>A,T), RS1001356938 (14:104987936 C>T), RS1001460218 (14:104988008 A>G), RS1001627335 (14:104984251 C>T), RS1001681036 (14:104983917 C>G), RS1001764234 (14:104987807 ATG>A,ATGTG), RS1002170764 (14:104987380 C>A,T), RS1002177952 (14:104998252 T>C,G), RS1002279262 (14:104992205 G>A), RS1002430911 (14:104997615 T>C)

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

2 associations (top):

Study	Trait	p-value
GCST007002_7	Cerebrospinal fluid t-tau levels in normal cognition	7.000000e-09
GCST007007_3	Cerebrospinal fluid t-tau levels	7.000000e-06

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0004760	t-tau measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	decreases expression	2
Aflatoxin B1	increases expression	2
aristolochic acid I	increases expression	1
bisphenol F	affects cotreatment, increases expression	1
sodium arsenate	decreases expression, increases abundance	1
ferrous chloride	decreases expression	1
di-n-butylphosphoric acid	affects expression	1
ICG 001	decreases expression	1
abrine	increases expression	1
bisphenol S	increases methylation	1
4-(4-((5-(4,5-dimethyl-2-nitrophenyl)-2-furanyl)methylene)-4,5-dihydro-3-methyl-5-oxo-1H-pyrazol-1-yl)benzoic acid	increases expression	1
Acetaminophen	decreases expression	1
Arsenic	decreases expression, increases abundance	1
Atrazine	decreases expression	1
Benzo(a)pyrene	decreases expression	1
Dexamethasone	affects cotreatment, increases expression	1
Indomethacin	affects cotreatment, increases expression	1
Methyl Methanesulfonate	increases expression	1
Rotenone	decreases expression	1
Smoke	decreases expression	1
Tetrachlorodibenzodioxin	affects expression	1
Thiram	decreases expression	1
Tobacco Smoke Pollution	decreases expression	1
Tretinoin	decreases expression	1
Urethane	decreases expression	1
Valproic Acid	increases methylation	1
1-Methyl-3-isobutylxanthine	affects cotreatment, increases expression	1
Cadmium Chloride	decreases expression	1
Okadaic Acid	decreases expression	1
Acrylamide	decreases expression	1

Clinical trials (associated diseases)

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