TBC1D22A

gene
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Summary

TBC1D22A (TBC1 domain family member 22A, HGNC:1309) is a protein-coding gene on chromosome 22q13.31, encoding TBC1 domain family member 22A (Q8WUA7). May act as a GTPase-activating protein for Rab family protein(s).

Enables 14-3-3 protein binding activity and protein homodimerization activity. Predicted to be active in Golgi apparatus.

Source: NCBI Gene 25771 — RefSeq curated summary.

At a glance

  • GWAS associations: 7
  • Clinical variants (ClinVar): 95 total
  • MANE Select transcript: NM_014346

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:1309
Approved symbolTBC1D22A
NameTBC1 domain family member 22A
Location22q13.31
Locus typegene with protein product
StatusApproved
Ensembl geneENSG00000054611
Ensembl biotypeprotein_coding
OMIM616879
Entrez25771

Gene structure

Transcript identifiers

Ensembl transcripts: 19 — 13 protein_coding, 3 nonsense_mediated_decay, 3 protein_coding_CDS_not_defined

ENST00000337137, ENST00000355704, ENST00000380995, ENST00000394449, ENST00000406733, ENST00000407381, ENST00000441162, ENST00000441936, ENST00000472791, ENST00000486163, ENST00000496139, ENST00000859789, ENST00000859790, ENST00000859791, ENST00000859792, ENST00000859793, ENST00000859794, ENST00000918112, ENST00000954015

RefSeq mRNA: 5 — MANE Select: NM_014346 NM_001284303, NM_001284304, NM_001284305, NM_001410803, NM_014346

CCDS: CCDS14078, CCDS63511, CCDS63512, CCDS74877, CCDS93180

Canonical transcript exons

ENST00000337137 — 13 exons

ExonStartEnd
ENSE000011455864687865346878723
ENSE000011455954679744446797620
ENSE000019165474676265046762848
ENSE000019365824717349847175693
ENSE000034724494689478446894846
ENSE000034806424711150847111603
ENSE000035055124699763446997709
ENSE000035387334679252046792576
ENSE000035600684679350146793841
ENSE000035816764689126646891394
ENSE000035866774691207446912188
ENSE000036167094697429046974399
ENSE000036287314703707147037198

Expression profiles

Bgee: expression breadth ubiquitous, 276 present calls, max score 96.66.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 33.1142 / max 308.3397, expressed in 1822 samples.

FANTOM5 promoters (6 alternative TSS)

Promoter IDTPM avgSamples expressed
19283530.56221820
1928360.7802489
1928370.6783243
1928390.5159249
1928400.4397229
2095140.137732

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
pancreatic ductal cellCL:000207996.66gold quality
cervix squamous epitheliumUBERON:000692292.44gold quality
amniotic fluidUBERON:000017392.07gold quality
epithelium of nasopharynxUBERON:000195190.88gold quality
gingival epitheliumUBERON:000194990.73gold quality
granulocyteCL:000009490.70gold quality
palpebral conjunctivaUBERON:000181290.33gold quality
ileal mucosaUBERON:000033190.21gold quality
squamous epitheliumUBERON:000691490.01gold quality
bloodUBERON:000017889.87gold quality
monocyteCL:000057689.80gold quality
leukocyteCL:000073889.71gold quality
mononuclear cellCL:000084289.66gold quality
colonic epitheliumUBERON:000039789.04gold quality
tongue squamous epitheliumUBERON:000691989.03gold quality
esophagus squamous epitheliumUBERON:000692088.93gold quality
epithelium of esophagusUBERON:000197688.69gold quality
sural nerveUBERON:001548888.53gold quality
gingivaUBERON:000182888.26gold quality
endothelial cellCL:000011588.21gold quality
mucosa of transverse colonUBERON:000499187.67gold quality
tonsilUBERON:000237287.25gold quality
germinal epithelium of ovaryUBERON:000130487.22gold quality
tibialis anteriorUBERON:000138587.08gold quality
esophagus mucosaUBERON:000246986.80gold quality
lower esophagus mucosaUBERON:003583486.68gold quality
gastrocnemiusUBERON:000138886.67gold quality
hair follicleUBERON:000207386.61silver quality
spleenUBERON:000210686.46gold quality
skin of legUBERON:000151186.36gold quality

Single-cell (SCXA)

Detected in 4 experiment(s), a significant marker in 4.

ExperimentMarker?Max mean expression
E-HCAD-35yes29.82
E-HCAD-25yes14.54
E-CURD-119yes6.49
E-ANND-3no0.00

Regulation

Is transcription factor: yes

Downstream targets (CollecTRI)

1 targets.

TargetRegulation
ACBD3Unknown

miRNA regulators (miRDB)

56 targeting TBC1D22A, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-6873-3P100.0071.422626
HSA-MIR-9-5P100.0072.282361
HSA-MIR-6833-3P100.0070.633197
HSA-MIR-4768-5P100.0069.492861
HSA-MIR-4510100.0066.602050
HSA-MIR-6127100.0066.762188
HSA-MIR-6129100.0066.462080
HSA-MIR-6130100.0066.692012
HSA-MIR-6133100.0066.482064
HSA-MIR-4262100.0073.263931
HSA-MIR-448799.9664.581252
HSA-MIR-426799.9666.532368
HSA-MIR-6508-5P99.9270.672465
HSA-MIR-182-5P99.8774.032589
HSA-MIR-92A-2-5P99.7567.012164
HSA-MIR-3680-3P99.7572.513095
HSA-MIR-361899.6968.571012
HSA-MIR-129099.5969.902079
HSA-MIR-211399.5871.221521
HSA-MIR-443799.5265.291266
HSA-MIR-4761-5P99.5166.69804
HSA-MIR-444199.4966.563216
HSA-MIR-132499.4666.571302
HSA-MIR-431899.3866.941505
HSA-MIR-431699.3765.751360
HSA-MIR-4685-5P99.2565.991563
HSA-MIR-6837-5P99.2565.471632
HSA-MIR-499A-3P99.1869.201392
HSA-MIR-499B-3P99.1869.271391
HSA-MIR-6809-5P99.1368.451223

Literature-anchored findings (GeneRIF, showing 3)

  • crystal structures of the first two mammalian TBCs, human TBC1 family members 22A (TBC1D22A) and 14 (TBC1D14) (PMID:18186464)
  • genetic association studies in population in Han Chinese: Data suggest that SNPs in TBC1D22A (rs7755450 and rs11758293) are associated with body mass index in obese females; other SNPs in TBC1D22A are associated with body mass index in obese males. (PMID:23526746)
  • Using affinity purification-mass spectrometry, we identified the putative Rab33 GTPase-activating proteins TBC1D22A and TBC1D22B as ACBD3-interacting factors. (PMID:23572552)

Cross-species orthologs

3 orthologs

OrganismSymbolGene ID
danio_reriotbc1d22aENSDARG00000045510
mus_musculusTbc1d22aENSMUSG00000051864
rattus_norvegicusTbc1d22aENSRNOG00000017057

Paralogs (45): RABGAP1 (ENSG00000011454), TBC1D22B (ENSG00000065491), TBC1D1 (ENSG00000065882), EVI5 (ENSG00000067208), TBC1D25 (ENSG00000068354), TBC1D2 (ENSG00000095383), TBC1D10A (ENSG00000099992), SGSM3 (ENSG00000100359), TBC1D17 (ENSG00000104946), TBC1D13 (ENSG00000107021), TBC1D12 (ENSG00000108239), TBC1D9 (ENSG00000109436), TBC1D30 (ENSG00000111490), TBC1D15 (ENSG00000121749), TBC1D5 (ENSG00000131374), TBC1D14 (ENSG00000132405), TBC1D8B (ENSG00000133138), TBC1D4 (ENSG00000136111), GRTP1 (ENSG00000139835), SGSM2 (ENSG00000141258), EVI5L (ENSG00000142459), TBCK (ENSG00000145348), USP6NL (ENSG00000148429), RABGAP1L (ENSG00000152061), SGSM1 (ENSG00000167037), TBC1D21 (ENSG00000167139), TBC1D2B (ENSG00000167202), TBC1D16 (ENSG00000167291), TBC1D10B (ENSG00000169221), TBC1D10C (ENSG00000175463), TBC1D28 (ENSG00000189375), TBC1D9B (ENSG00000197226), TBC1D8 (ENSG00000204634), TBC1D26 (ENSG00000214946), TBC1D3G (ENSG00000260287), TBC1D3K (ENSG00000273513), TBC1D3H (ENSG00000274226), TBC1D3D (ENSG00000274419), TBC1D3L (ENSG00000274512), TBC1D3 (ENSG00000274611)

Protein

Protein identifiers

TBC1 domain family member 22AQ8WUA7 (reviewed: Q8WUA7)

All UniProt accessions (5): A0A0A0MRY0, B0QYI1, Q8WUA7, F8WBF7, F8WDP1

UniProt curated annotations — full annotation on UniProt →

Function. May act as a GTPase-activating protein for Rab family protein(s).

Subunit / interactions. Homodimer. Interacts with ACBD3 and ARFGEF1. Interacts with YWHAB, YWHAE, YWHAG, YWHAH, YWHAQ and YWHAZ.

Isoforms (4)

UniProt IDNamesCanonical?
Q8WUA7-11yes
Q8WUA7-22
Q8WUA7-33
Q8WUA7-44

RefSeq proteins (5): NP_001271232, NP_001271233, NP_001271234, NP_001397732, NP_055161* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR000195Rab-GAP-TBC_domDomain
IPR035969Rab-GAP_TBC_sfHomologous_superfamily

Pfam: PF00566

UniProt features (58 total): helix 22, mutagenesis site 15, splice variant 5, modified residue 4, sequence conflict 3, turn 3, compositionally biased region 2, initiator methionine 1, chain 1, domain 1, region of interest 1

Structure

Experimental structures (PDB)

1 structures.

PDBMethodResolution (Å)
2QFZX-RAY DIFFRACTION2.1

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q8WUA7-F177.510.61

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 (4): 2, 132, 145, 167

Mutagenesis-validated functional residues (15):

PositionPhenotype
90–92no effect on acbd3-binding.
92–93no effect on interaction with acbd3, nor with 14-3-3 proteins.
93–96decreased acbd3-binding.
96–97no effect on acbd3-binding.
99–100no effect on acbd3-binding.
101–102drastically decreased acbd3-binding. no effect on binding to 14-3-3 protein.
103–105no effect on acbd3-binding.
132no effect on 14-3-3 protein-binding.
149–150decreased 14-3-3 protein-binding.
165–167complete loss of 14-3-3 protein-binding.
165no effect on interaction with acbd3. decreased 14-3-3 protein-binding.
165complete loss of 14-3-3 protein-binding.
167complete loss of 14-3-3 protein-binding.
320decreased 14-3-3 protein-binding.

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 182 (showing top): RRAGTTGT_UNKNOWN, MORF_FLT1, PAX4_01, MORF_MSH3, LFA1_Q6, MORF_BRCA1, MORF_ATRX, TGACCTY_ERR1_Q2, MORF_ESR1, GOBP_REGULATION_OF_CELLULAR_COMPONENT_BIOGENESIS, RICKMAN_METASTASIS_DN, GOBP_REGULATION_OF_CELL_PROJECTION_ORGANIZATION, GOBP_CILIUM_ORGANIZATION, KINSEY_TARGETS_OF_EWSR1_FLII_FUSION_DN, GOBP_ORGANELLE_ASSEMBLY

GO Biological Process (0):

GO Molecular Function (4): GTPase activator activity (GO:0005096), protein homodimerization activity (GO:0042803), 14-3-3 protein binding (GO:0071889), protein binding (GO:0005515)

GO Cellular Component (1): Golgi apparatus (GO:0005794)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
GTPase activity1
enzyme activator activity1
GTPase regulator activity1
identical protein binding1
protein dimerization activity1
protein binding1
binding1
cytoplasm1
endomembrane system1
intracellular membrane-bounded organelle1

Protein interactions and networks

STRING

1633 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
TBC1D22AGRTP1Q5TC63588
TBC1D22ATBC1D20Q96BZ9586
TBC1D22ATRABDQ9H4I3549
TBC1D22ATBC1D21Q8IYX1542
TBC1D22ATBC1D8BQ0IIM8539
TBC1D22ATBC1D19Q8N5T2522
TBC1D22AMON2Q7Z3U7503
TBC1D22ARBM12BQ8IXT5491
TBC1D22AMOSPD3O75425485
TBC1D22ATBC1D10CQ8IV04482
TBC1D22ATBC1D8O95759464
TBC1D22ASLC38A10Q9HBR0461
TBC1D22ATBC1D9BQ66K14457
TBC1D22API4KBP78405454
TBC1D22AZNF516Q92618449

IntAct

31 interactions, top by confidence:

ABTypeScore
ACBD3TBC1D22Apsi-mi:“MI:0915”(physical association)0.720
TBC1D22AACBD3psi-mi:“MI:0915”(physical association)0.720
YWHABBLTP3Bpsi-mi:“MI:0914”(association)0.610
ACBD3PI4KBpsi-mi:“MI:0914”(association)0.570
TBC1D22BA2ML1psi-mi:“MI:0914”(association)0.530
DNAJB8DNAJB6psi-mi:“MI:0914”(association)0.530
TBC1D22Apsi-mi:“MI:0914”(association)0.460
TBC1D22ASTT3Bpsi-mi:“MI:0915”(physical association)0.400
CERKWDR46psi-mi:“MI:0914”(association)0.350
ACBD3PIP4P1psi-mi:“MI:0914”(association)0.350
ACBD3BCKDHBpsi-mi:“MI:0914”(association)0.350
TBC1D22AVPS26Apsi-mi:“MI:0914”(association)0.350
TBC1D22Apsi-mi:“MI:0914”(association)0.350
TACSTD2RIMOC1psi-mi:“MI:0914”(association)0.350
TBC1D22AACSL4psi-mi:“MI:0914”(association)0.350
TBC1D22ACTSVpsi-mi:“MI:0914”(association)0.350
AURKBVWA8psi-mi:“MI:0914”(association)0.350
CD33SPAG9psi-mi:“MI:0914”(association)0.350
CLEC4CENTPD6psi-mi:“MI:0914”(association)0.350
CREB3L2PLEKHG3psi-mi:“MI:0914”(association)0.350
EPHA1ENC1psi-mi:“MI:0914”(association)0.350
RIC3QSOX1psi-mi:“MI:0914”(association)0.350
SCN2BRIMOC1psi-mi:“MI:0914”(association)0.350
TGOLN2BLTP3Bpsi-mi:“MI:2364”(proximity)0.270
TBC1D22Apsi-mi:“MI:0915”(physical association)0.000

BioGRID (69): HSPA1L (Affinity Capture-MS), ACBD3 (Affinity Capture-MS), FDXR (Affinity Capture-MS), ACSL4 (Affinity Capture-MS), FLYWCH2 (Affinity Capture-MS), BIRC6 (Affinity Capture-MS), ARFGEF1 (Affinity Capture-MS), QSOX2 (Affinity Capture-MS), MICU1 (Affinity Capture-MS), KIRREL (Affinity Capture-MS), MICU2 (Affinity Capture-MS), DNAJB4 (Affinity Capture-MS), SUPT6H (Affinity Capture-MS), EFNB3 (Affinity Capture-MS), EPHA4 (Affinity Capture-MS)

ESM2 similar proteins: A0FI79, A1A4I4, A1A5B6, A4D2P6, A6H7I8, F1LXF1, O60346, P11274, P53349, P59672, P70268, Q0QWG9, Q13905, Q3MII6, Q3U0J8, Q504T8, Q50H33, Q5EBH1, Q62865, Q63433, Q69ZT9, Q6NS60, Q6PAJ1, Q6WVG3, Q6ZWB6, Q7Z5H3, Q8BL80, Q8BUP8, Q8BYH7, Q8C190, Q8CGA2, Q8CHE4, Q8N2R8, Q8R554, Q8TE49, Q8TF61, Q8WUA7, Q92625, Q95KI1, Q96CX2

Diamond homologs: O59737, Q08484, Q8R5A6, Q8WUA7, Q95KI1, Q95LL3, Q9NU19, Q54VM3, Q8R3D1, Q9NVG8

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance71
Likely benign6
Benign3

Top pathogenic / likely-pathogenic (0)

SpliceAI

7544 predictions. Top by Δscore:

VariantEffectΔscore
22:46792577:G:GGdonor_gain1.0000
22:46793499:A:AGacceptor_gain1.0000
22:46793499:AGTTT:Aacceptor_gain1.0000
22:46793500:G:GTacceptor_gain1.0000
22:46793500:GT:Gacceptor_gain1.0000
22:46793500:GTT:Gacceptor_gain1.0000
22:46793500:GTTT:Gacceptor_gain1.0000
22:46793500:GTTTG:Gacceptor_gain1.0000
22:46793839:CAGG:Cdonor_loss1.0000
22:46793840:AGGT:Adonor_loss1.0000
22:46793841:GGTA:Gdonor_loss1.0000
22:46793842:G:GCdonor_loss1.0000
22:46793843:T:Adonor_loss1.0000
22:46797618:TTGGT:Tdonor_loss1.0000
22:46797621:G:GCdonor_loss1.0000
22:46797621:G:GGdonor_gain1.0000
22:46797622:T:Adonor_loss1.0000
22:46878651:A:AGacceptor_gain1.0000
22:46878652:G:GGacceptor_gain1.0000
22:46878724:G:GGdonor_gain1.0000
22:46891392:CAG:Cdonor_loss1.0000
22:46891395:GTG:Gdonor_loss1.0000
22:46912072:A:AGacceptor_gain1.0000
22:46912072:AG:Aacceptor_loss1.0000
22:46912073:G:GAacceptor_gain1.0000
22:46912073:GA:Gacceptor_gain1.0000
22:46912073:GAT:Gacceptor_gain1.0000
22:46912073:GATT:Gacceptor_gain1.0000
22:46912185:ATAGG:Adonor_loss1.0000
22:46912187:AGGT:Adonor_loss1.0000

AlphaMissense

3437 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
22:46912134:G:CG321R1.000
22:47037124:T:CF419L1.000
22:47037126:C:AF419L1.000
22:47037126:C:GF419L1.000
22:47037130:T:AW421R1.000
22:47037130:T:CW421R1.000
22:47037152:G:TR428M1.000
22:46878709:T:AW232R0.999
22:46878709:T:CW232R0.999
22:46891326:T:GY257D0.999
22:46894795:C:AD283E0.999
22:46894795:C:GD283E0.999
22:46912101:G:CA310P0.999
22:46912108:G:CR312P0.999
22:46912110:C:GH313D0.999
22:46912125:T:CY318H0.999
22:46912129:T:AV319D0.999
22:46912133:G:CQ320H0.999
22:46912133:G:TQ320H0.999
22:46912134:G:TG321C0.999
22:46912142:T:AN323K0.999
22:46912142:T:GN323K0.999
22:47037118:T:CF417L0.999
22:47037120:T:AF417L0.999
22:47037120:T:GF417L0.999
22:47037125:T:CF419S0.999
22:47037125:T:GF419C0.999
22:47037138:C:AN423K0.999
22:47037138:C:GN423K0.999
22:47037141:C:AN424K0.999

dbSNP variants (sampled 300 via entrez): RS1000000544 (22:47163450 C>T), RS1000003756 (22:47041266 C>G,T), RS1000009391 (22:47157717 G>GCACA), RS1000030084 (22:46838524 A>G,T), RS1000033260 (22:47041405 T>A), RS1000041121 (22:47098556 T>A), RS1000048133 (22:46867960 A>G), RS1000048546 (22:46971635 G>C,T), RS1000050421 (22:46985512 T>C), RS1000051865 (22:46944396 C>T), RS1000055459 (22:47110736 G>A), RS1000055636 (22:46843487 G>A,C), RS1000073319 (22:46797557 G>A), RS1000078023 (22:46761527 G>T), RS1000081674 (22:47149945 G>A)

Disease associations

OMIM: gene MIM:616879 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

7 associations (top):

StudyTraitp-value
GCST000785_25Longevity1.000000e-06
GCST001585_4Breast size7.000000e-06
GCST003478_4Hair greying5.000000e-06
GCST004351_28Bone ultrasound measurement (broadband ultrasound attenuation)2.000000e-07
GCST009086_4Pneumococcal meningitis6.000000e-07
GCST009391_1684Metabolite levels4.000000e-06
GCST90093325_20Language functional connectivity3.000000e-12

EFO canonical traits (3, from GWAS)

EFO IDTrait name
EFO:0004514bone quantitative ultrasound measurement
EFO:0010343cholesteryl ester 18:0 measurement
EFO:0007797language measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
Benzo(a)pyreneaffects methylation, decreases expression7
Aflatoxin B1decreases expression, decreases methylation, increases methylation, affects expression4
bisphenol Adecreases expression, decreases methylation, affects cotreatment, increases methylation2
aristolochic acid Idecreases expression1
FR900359decreases phosphorylation1
triphenyl phosphateaffects expression1
sodium arsenitedecreases expression1
zinc chromateincreases abundance, decreases expression1
benzo(e)pyreneaffects methylation1
aflatoxin B2affects methylation1
coumarindecreases phosphorylation1
1-hydroxypyreneaffects cotreatment, decreases methylation1
chromium hexavalent iondecreases expression, increases abundance1
pentabromodiphenyl etherincreases expression1
CGP 52608affects binding, increases reaction1
2,2’,4,4’-tetrabromodiphenyl etherincreases expression1
3-(2-hydroxy-4-(2-methylnonan-2-yl)phenyl)cyclohexan-1-oldecreases expression1
Fulvestrantaffects cotreatment, increases methylation1
Acetaminophendecreases expression1
Air Pollutantsaffects expression, increases abundance1
Arsenicaffects methylation1
Caffeinedecreases phosphorylation1
Carcinogensdecreases expression1
Cisplatindecreases expression1
Doxorubicinaffects expression1
Formaldehydedecreases expression1
Ivermectindecreases expression1
Methapyrileneaffects methylation1
Mutagensdecreases expression1
Ozoneincreases abundance, affects expression1

Clinical trials (associated diseases)

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

  • Disease cohort memberships (association, not causation — diseases whose associated-gene cohort lists this gene; a subset are also under Associated diseases): pneumococcal meningitis