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TAFA2

gene
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Also known as TAFA-2

Summary

TAFA2 (TAFA chemokine like family member 2, HGNC:21589) is a protein-coding gene on chromosome 12q14.1, encoding Chemokine-like protein TAFA-2 (Q8N3H0). Has a role as neurotrophic factor involved in neuronal survival and neurobiological functions.

This gene is a member of the TAFA family which is composed of five highly homologous genes that encode small secreted proteins. These proteins contain conserved cysteine residues at fixed positions, and are distantly related to MIP-1alpha, a member of the CC-chemokine family. The TAFA proteins are predominantly expressed in specific regions of the brain, and are postulated to function as brain-specific chemokines or neurokines, that act as regulators of immune and nervous cells.

Source: NCBI Gene 338811 — RefSeq curated summary.

At a glance

  • GWAS associations: 55
  • Clinical variants (ClinVar): 21 total
  • MANE Select transcript: NM_178539

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:21589
Approved symbolTAFA2
NameTAFA chemokine like family member 2
Location12q14.1
Locus typegene with protein product
StatusApproved
AliasesTAFA-2
Ensembl geneENSG00000198673
Ensembl biotypeprotein_coding
OMIM617496
Entrez338811

Gene structure

Transcript identifiers

Ensembl transcripts: 19 — 10 protein_coding, 6 protein_coding_CDS_not_defined, 2 retained_intron, 1 nonsense_mediated_decay

ENST00000416284, ENST00000500610, ENST00000547075, ENST00000547919, ENST00000547941, ENST00000548541, ENST00000548780, ENST00000549379, ENST00000549456, ENST00000549958, ENST00000550003, ENST00000550060, ENST00000550396, ENST00000551449, ENST00000551619, ENST00000552075, ENST00000873975, ENST00000957716, ENST00000957717

RefSeq mRNA: 1 — MANE Select: NM_178539 NM_178539

CCDS: CCDS8962

Canonical transcript exons

ENST00000416284 — 5 exons

ExonStartEnd
ENSE000023179386219125962192773
ENSE000023268256170827361710417
ENSE000035146606175362261753746
ENSE000035675406186732061867426
ENSE000037859296175487261755024

Expression profiles

Bgee: expression breadth ubiquitous, 201 present calls, max score 93.34.

FANTOM5 (CAGE): breadth broad, TPM avg 3.3736 / max 172.2434, expressed in 652 samples.

FANTOM5 promoters (16 alternative TSS)

Promoter IDTPM avgSamples expressed
1318180.6888365
1318120.4598137
1318020.352291
1318040.331684
1318050.236366
1318090.223481
1318100.200888
1318170.187176
1318110.152170
1318160.128053

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
secondary oocyteCL:000065593.34gold quality
buccal mucosa cellCL:000233693.13gold quality
primary visual cortexUBERON:000243692.97gold quality
endothelial cellCL:000011592.16gold quality
occipital lobeUBERON:000202190.79gold quality
Brodmann (1909) area 23UBERON:001355490.53gold quality
middle temporal gyrusUBERON:000277190.51gold quality
prefrontal cortexUBERON:000045188.92gold quality
dorsolateral prefrontal cortexUBERON:000983488.60gold quality
Brodmann (1909) area 9UBERON:001354087.94gold quality
Brodmann (1909) area 46UBERON:000648387.70gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047387.46gold quality
frontal cortexUBERON:000187087.21gold quality
neocortexUBERON:000195087.08gold quality
superior frontal gyrusUBERON:000266186.74gold quality
anterior cingulate cortexUBERON:000983586.49gold quality
cerebral cortexUBERON:000095686.31gold quality
left testisUBERON:000453386.24gold quality
right testisUBERON:000453485.70gold quality
entorhinal cortexUBERON:000272885.57gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099184.82gold quality
postcentral gyrusUBERON:000258184.64gold quality
temporal lobeUBERON:000187184.55gold quality
right frontal lobeUBERON:000281084.53gold quality
cortical plateUBERON:000534384.43gold quality
testisUBERON:000047384.35gold quality
parietal lobeUBERON:000187284.12gold quality
amygdalaUBERON:000187683.80gold quality
monocyteCL:000057682.59gold quality
leukocyteCL:000073882.07gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-HCAD-35yes67.82
E-ANND-3yes7.18

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

166 targeting TAFA2, 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-4262100.0073.263931
HSA-MIR-3163100.0077.238605
HSA-MIR-5692B100.0071.322622
HSA-MIR-5692C100.0071.322622
HSA-MIR-4668-3P100.0068.742635
HSA-MIR-366299.9973.825684
HSA-MIR-548C-3P99.9974.017587
HSA-MIR-181A-5P99.9972.962995
HSA-MIR-181B-5P99.9972.972996
HSA-MIR-181C-5P99.9972.952996
HSA-MIR-181D-5P99.9973.042997
HSA-MIR-186-5P99.9970.833707
HSA-MIR-371B-5P99.9975.344759
HSA-MIR-4482-3P99.9872.503147
HSA-MIR-520D-5P99.9873.344883
HSA-MIR-524-5P99.9873.434882
HSA-MIR-1213699.9872.815713
HSA-MIR-548N99.9871.944170
HSA-MIR-548P99.9872.253784
HSA-MIR-56899.9869.862084
HSA-MIR-480399.9871.993117
HSA-MIR-373-5P99.9875.364753
HSA-MIR-616-5P99.9875.584775
HSA-MIR-569699.9872.364487
HSA-MIR-302C-5P99.9772.563642
HSA-MIR-60799.9773.625593
HSA-MIR-590-3P99.9674.346478
HSA-MIR-568899.9673.234504
HSA-MIR-495-3P99.9672.814197
HSA-MIR-426799.9666.532368

Literature-anchored findings (GeneRIF, showing 3)

  • Variants of FAM19A2 (rs348644) are associated with forced expiratory volume in COPD. (PMID:25112515)
  • Data identified two, BCL2 and FAM19A2, novel loci and replicated known variants associated with insulin sensitivity. Further studies are needed to clarify the causal variant and function at the BCL2 and FAM19A2 loci. (PMID:27416945)
  • interleukin-1beta was found as an upstream regulator of TAFA2 expression. Our findings demonstrate that TAFA2 enhances hMSC migration and recruitment and thus is relevant for regenerative medicine applications. (PMID:30485583)

Cross-species orthologs

2 orthologs

OrganismSymbolGene ID
mus_musculusTafa2ENSMUSG00000044071
rattus_norvegicusTafa2ENSRNOG00000064852

Paralogs (3): TAFA4 (ENSG00000163377), TAFA1 (ENSG00000183662), TAFA3 (ENSG00000184599)

Protein

Protein identifiers

Chemokine-like protein TAFA-2 — Q8N3H0 (reviewed: Q8N3H0)

All UniProt accessions (6): A0A0C4DGI5, Q8N3H0, F8VVD7, F8VVF9, F8VWB2, F8VZY8

UniProt curated annotations — full annotation on UniProt →

Function. Has a role as neurotrophic factor involved in neuronal survival and neurobiological functions.

Subcellular location. Cytoplasm. Nucleus.

Tissue specificity. Brain-specific.

Similarity. Belongs to the TAFA family.

Isoforms (2)

UniProt IDNamesCanonical?
Q8N3H0-11yes
Q8N3H0-22

RefSeq proteins (1): NP_848634* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR020350Chemokine-like_TAFAFamily
IPR051743TAFA_chemokine-likeFamily

Pfam: PF12020

UniProt features (6 total): sequence conflict 3, signal peptide 1, chain 1, splice variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q8N3H0-F187.990.63

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 150 (showing top): GSE18804_SPLEEN_MACROPHAGE_VS_BRAIN_TUMORAL_MACROPHAGE_UP, GOBP_MEMORY, GOBP_COGNITION, GOBP_BEHAVIOR, GOBP_ASSOCIATIVE_LEARNING, GGAMTNNNNNTCCY_UNKNOWN, MAYBURD_RESPONSE_TO_L663536_UP, GOBP_LEARNING, GOBP_RESPONSE_TO_RADIATION, GOBP_RESPONSE_TO_ABIOTIC_STIMULUS, DOUGLAS_BMI1_TARGETS_DN, AACTTT_UNKNOWN, GOBP_VISUAL_BEHAVIOR, E12_Q6, DBP_Q6

GO Biological Process (3): memory (GO:0007613), visual learning (GO:0008542), signal transduction (GO:0007165)

GO Molecular Function (1): receptor ligand activity (GO:0048018)

GO Cellular Component (3): obsolete extracellular space (GO:0005615), nucleus (GO:0005634), cytoplasm (GO:0005737)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
learning or memory1
visual behavior1
associative learning1
cell communication1
cellular process1
signaling1
regulation of cellular process1
cellular response to stimulus1
signaling receptor binding1
signal transduction1
signaling receptor activator activity1
intracellular membrane-bounded organelle1
intracellular anatomical structure1
cellular anatomical structure1

Protein interactions and networks

STRING

509 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
TAFA2KBTBD12Q3ZCT8545
TAFA2NALF1B1AL88529
TAFA2NAALADL2Q58DX5525
TAFA2ARMH2H3BNL8475
TAFA2ERICH3Q5RHP9472
TAFA2CWF19L2Q2TBE0470
TAFA2TMEM161BQ8NDZ6455
TAFA2IMMP2LQ96T52433
TAFA2IQSEC3Q9UPP2411
TAFA2CEP170BQ9Y4F5407
TAFA2BCO2Q9BYV7397
TAFA2OR8D4Q8NGM9393
TAFA2TMEM117Q9H0C3392
TAFA2ZMYND12Q9H0C1390
TAFA2TOMM70O94826389

IntAct

2 interactions, top by confidence:

ABTypeScore
TAFA2ERN1psi-mi:“MI:0914”(association)0.350

BioGRID (47): FAM19A2 (Affinity Capture-RNA), FAM19A2 (Synthetic Lethality), LEPR (Affinity Capture-MS), FREM2 (Affinity Capture-MS), NLGN2 (Affinity Capture-MS), INSR (Affinity Capture-MS), TMEM67 (Affinity Capture-MS), ATRNL1 (Affinity Capture-MS), TXNDC16 (Affinity Capture-MS), SUSD1 (Affinity Capture-MS), VWDE (Affinity Capture-MS), COL6A2 (Affinity Capture-MS), CPE (Affinity Capture-MS), M6PR (Affinity Capture-MS), CNTNAP1 (Affinity Capture-MS)

ESM2 similar proteins: A0A023FBW7, A0A023FDY8, A0A023FFB5, A0A023FT45, A0A023G6B6, A0A023G9N9, A8CZZ0, A8CZZ1, A8CZZ8, B7XFU7, B7XFU8, C8BKF2, C8BKF3, G3MIX6, G3MJ83, L7M8Z8, O35736, O70514, P08505, P0C7L1, P0C8E7, P15514, P20607, P20826, P21581, P21583, P26893, P79169, P79368, Q06220, Q09108, Q09TK9, Q14512, Q28132, Q29030, Q5R6N2, Q6X784, Q802A9, Q8MUP7, Q8N3H0

Diamond homologs: M0R7X9, Q3ZBS2, Q5R6N2, Q7TPG5, Q7TPG6, Q7TPG7, Q7TPG8, Q7Z5A7, Q7Z5A8, Q7Z5A9, Q8N3H0, Q91WE9, Q96LR4, Q9N0D3

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance13
Likely benign0
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

4181 predictions. Top by Δscore:

VariantEffectΔscore
12:61710415:TACCT:Tacceptor_loss1.0000
12:61710416:ACC:Aacceptor_loss1.0000
12:61710418:CT:Cacceptor_loss1.0000
12:61753620:AC:Adonor_gain1.0000
12:61753621:CC:Cdonor_gain1.0000
12:61753747:C:CCacceptor_gain1.0000
12:61753749:A:Cacceptor_gain1.0000
12:61754829:T:TAdonor_gain1.0000
12:61867314:GCTTA:Gdonor_loss1.0000
12:61867315:CTTA:Cdonor_loss1.0000
12:61867316:TTA:Tdonor_loss1.0000
12:61867317:TA:Tdonor_loss1.0000
12:61867423:CATC:Cacceptor_gain1.0000
12:61930699:A:ACdonor_gain1.0000
12:61930700:C:CCdonor_gain1.0000
12:62089002:T:TAdonor_gain1.0000
12:62145566:ATCCT:Adonor_gain1.0000
12:62260490:A:Tdonor_gain1.0000
12:62260501:CTGGT:Cdonor_loss1.0000
12:62260503:GGT:Gdonor_loss1.0000
12:62260504:G:GGdonor_gain1.0000
12:62260504:G:Tdonor_loss1.0000
12:62260505:T:Gdonor_loss1.0000
12:61710413:GTTAC:Gacceptor_gain0.9900
12:61710414:TTAC:Tacceptor_gain0.9900
12:61710415:TAC:Tacceptor_gain0.9900
12:61710418:C:CCacceptor_gain0.9900
12:61753614:CCACT:Cdonor_loss0.9900
12:61753615:CACTT:Cdonor_loss0.9900
12:61753616:ACTTA:Adonor_loss0.9900

AlphaMissense

849 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
12:61753658:C:AW116C1.000
12:61753658:C:GW116C1.000
12:61753660:A:GW116R1.000
12:61753660:A:TW116R1.000
12:61753686:C:GC107S1.000
12:61753687:A:TC107S1.000
12:61753721:C:AW95C1.000
12:61753721:C:GW95C1.000
12:61753723:A:GW95R1.000
12:61753723:A:TW95R1.000
12:61754880:C:GC84S1.000
12:61754881:A:TC84S1.000
12:61754904:C:TG76D1.000
12:61754905:C:AG76C1.000
12:61754924:G:CC69W1.000
12:61754931:C:GC67S1.000
12:61754932:A:TC67S1.000
12:61753652:A:CC118W0.999
12:61753653:C:GC118S0.999
12:61753653:C:TC118Y0.999
12:61753654:A:GC118R0.999
12:61753654:A:TC118S0.999
12:61753663:C:GG115R0.999
12:61753663:C:TG115R0.999
12:61753687:A:GC107R0.999
12:61753703:A:CC101W0.999
12:61753704:C:GC101S0.999
12:61753705:A:GC101R0.999
12:61753705:A:TC101S0.999
12:61753707:G:TP100Q0.999

dbSNP variants (sampled 300 via entrez): RS1000009819 (12:62166911 A>G), RS1000012486 (12:61932171 T>A,C), RS1000018807 (12:61751953 C>T), RS1000029099 (12:62260261 C>G,T), RS1000033224 (12:62049174 C>T), RS1000039037 (12:61902029 G>A), RS1000058628 (12:62120505 C>G), RS1000061484 (12:62124693 T>C), RS1000064775 (12:61801636 G>A), RS1000072347 (12:61807590 G>C), RS1000081465 (12:61782205 A>G,T), RS1000084538 (12:61879876 A>T), RS1000093179 (12:61912146 G>T), RS1000095122 (12:61838670 A>G), RS1000101833 (12:61966761 A>G)

Disease associations

OMIM: gene MIM:617496 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

55 associations (top):

StudyTraitp-value
GCST000960_13Cardiac hypertrophy2.000000e-06
GCST001762_156Obesity-related traits5.000000e-06
GCST001762_382Obesity-related traits5.000000e-07
GCST002322_20Asthma and hay fever2.000000e-06
GCST002351_5Chronic obstructive pulmonary disease (moderate to severe)8.000000e-07
GCST002366_7Response to anti-retroviral therapy (ddI/d4T) in HIV-1 infection (Grade 1 peripheral neuropathy)9.000000e-06
GCST002761_15Hippocampal volume7.000000e-06
GCST003126_6Influenza A (H1N1) severity5.000000e-06
GCST003264_1364Post bronchodilator FEV1/FVC ratio6.000000e-08
GCST003264_1372Post bronchodilator FEV1/FVC ratio8.000000e-08
GCST003264_1374Post bronchodilator FEV1/FVC ratio8.000000e-08
GCST003264_1375Post bronchodilator FEV1/FVC ratio8.000000e-08
GCST003265_199Post bronchodilator FEV1/FVC ratio in COPD2.000000e-06
GCST003265_200Post bronchodilator FEV1/FVC ratio in COPD2.000000e-06
GCST003265_201Post bronchodilator FEV1/FVC ratio in COPD3.000000e-06
GCST003265_202Post bronchodilator FEV1/FVC ratio in COPD2.000000e-06
GCST003265_203Post bronchodilator FEV1/FVC ratio in COPD2.000000e-06
GCST003265_204Post bronchodilator FEV1/FVC ratio in COPD2.000000e-06
GCST003265_207Post bronchodilator FEV1/FVC ratio in COPD2.000000e-06
GCST003265_208Post bronchodilator FEV1/FVC ratio in COPD2.000000e-06
GCST003265_209Post bronchodilator FEV1/FVC ratio in COPD2.000000e-06
GCST003265_210Post bronchodilator FEV1/FVC ratio in COPD2.000000e-06
GCST003265_211Post bronchodilator FEV1/FVC ratio in COPD1.000000e-06
GCST003265_233Post bronchodilator FEV1/FVC ratio in COPD4.000000e-06
GCST003265_234Post bronchodilator FEV1/FVC ratio in COPD3.000000e-06
GCST003265_235Post bronchodilator FEV1/FVC ratio in COPD3.000000e-06
GCST003265_236Post bronchodilator FEV1/FVC ratio in COPD3.000000e-06
GCST003265_237Post bronchodilator FEV1/FVC ratio in COPD5.000000e-06
GCST003265_238Post bronchodilator FEV1/FVC ratio in COPD3.000000e-06
GCST003265_239Post bronchodilator FEV1/FVC ratio in COPD3.000000e-06

EFO canonical traits (14, from GWAS)

EFO IDTrait name
EFO:0002503cardiac hypertrophy
EFO:0004338body weight
EFO:0004340body mass index
EFO:0000180HIV-1 infection
EFO:0005035hippocampal volume
EFO:0007743influenza A severity measurement
EFO:0004713FEV/FVC ratio
EFO:0004471insulin sensitivity measurement
EFO:0007965response to combination chemotherapy
EFO:0007985platelet crit
EFO:0006336diastolic blood pressure
EFO:0006527smoking status measurement
EFO:0008354cognitive function measurement
EFO:0600011Parkinson’s disease symptom measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
Valproic Acidincreases expression, affects expression, affects cotreatment5
bisphenol Aincreases methylation, affects cotreatment, increases expression, decreases expression2
mercuric bromideincreases expression, affects cotreatment2
entinostatincreases expression, affects cotreatment2
belinostatincreases expression, affects cotreatment2
Benzo(a)pyreneaffects methylation, increases mutagenesis2
bisphenol Faffects cotreatment, increases expression1
sotorasibaffects cotreatment, increases expression1
methyleugenoldecreases expression1
triphenyl phosphateaffects expression1
arseniteincreases methylation1
sodium arseniteincreases expression1
di-n-butylphosphoric acidaffects expression1
CGP 52608increases reaction, affects binding1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, increases expression1
clothianidindecreases expression1
abrineincreases expression1
dorsomorphinaffects cotreatment, increases expression1
bisphenol Sdecreases methylation1
trametinibaffects cotreatment, increases expression1
NVP-BKM120affects cotreatment, increases expression1
Sunitinibdecreases expression1
Vehicle Emissionsdecreases methylation1
Dexamethasoneaffects cotreatment, increases expression1
Diethylhexyl Phthalateincreases expression1
Indomethacinaffects cotreatment, increases expression1
Methotrexatedecreases expression1
N-Nitrosopyrrolidinedecreases expression1
Nickeldecreases expression1
Progesteroneincreases expression1

Clinical trials (associated diseases)

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

About this page

Generated deterministically by Sugi Atlas from primary biomedical databases via BioBTree. Every record on this page traces to a primary source.

Generated
Atlas version
v1.1.2
BioBTree
v2.0.2

Sources 74

This page pulls from 74 datasets indexed by BioBTree:

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