FAM98A

gene
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Also known as DKFZP564F0522

Summary

FAM98A (family with sequence similarity 98 member A, HGNC:24520) is a protein-coding gene on chromosome 2p22.3, encoding Protein FAM98A (Q8NCA5). Positively stimulates PRMT1-induced protein arginine methylation.

Enables protein methyltransferase activity. Involved in positive regulation of cell population proliferation; positive regulation of gene expression; and protein methylation. Predicted to be located in cytoplasm and nucleus. Predicted to be part of tRNA-splicing ligase complex.

Source: NCBI Gene 25940 — RefSeq curated summary.

At a glance

  • GWAS associations: 9
  • Clinical variants (ClinVar): 87 total
  • MANE Select transcript: NM_015475

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:24520
Approved symbolFAM98A
Namefamily with sequence similarity 98 member A
Location2p22.3
Locus typegene with protein product
StatusApproved
AliasesDKFZP564F0522
Ensembl geneENSG00000119812
Ensembl biotypeprotein_coding
OMIM620904
Entrez25940

Gene structure

Transcript identifiers

Ensembl transcripts: 18 — 8 retained_intron, 5 nonsense_mediated_decay, 4 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000238823, ENST00000403368, ENST00000437680, ENST00000464415, ENST00000474985, ENST00000475122, ENST00000492649, ENST00000685835, ENST00000687030, ENST00000689312, ENST00000689698, ENST00000689713, ENST00000690423, ENST00000690429, ENST00000692348, ENST00000692917, ENST00000693631, ENST00000693737

RefSeq mRNA: 2 — MANE Select: NM_015475 NM_001304538, NM_015475

CCDS: CCDS33179, CCDS92735

Canonical transcript exons

ENST00000238823 — 8 exons

ExonStartEnd
ENSE000016987923358833533588519
ENSE000018990853359916933599299
ENSE000019281553358366033585444
ENSE000034639573358553033585697
ENSE000035477343359548933595637
ENSE000035907483358656233586678
ENSE000036088063358724033587320
ENSE000036690553359208033592214

Expression profiles

Bgee: expression breadth ubiquitous, 297 present calls, max score 97.25.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 29.7496 / max 797.7526, expressed in 1802 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter IDTPM avgSamples expressed
2771926.76031799
277182.73081373
277200.2585103

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
tibiaUBERON:000097997.25gold quality
male germ cellCL:000001596.02gold quality
spermCL:000001995.83gold quality
esophagus squamous epitheliumUBERON:000692095.81gold quality
smooth muscle tissueUBERON:000113595.39gold quality
ponsUBERON:000098895.35gold quality
inferior vagus X ganglionUBERON:000536395.33gold quality
heart right ventricleUBERON:000208095.07gold quality
biceps brachiiUBERON:000150795.00gold quality
epithelium of esophagusUBERON:000197694.96gold quality
endothelial cellCL:000011594.92silver quality
choroid plexus epitheliumUBERON:000391194.92gold quality
skeletal muscle tissue of biceps brachiiUBERON:000450294.90gold quality
lateral nuclear group of thalamusUBERON:000273694.74gold quality
Brodmann (1909) area 46UBERON:000648394.69gold quality
stromal cell of endometriumCL:000225594.66gold quality
skeletal muscle tissue of rectus abdominisUBERON:000451194.52gold quality
dorsal plus ventral thalamusUBERON:000189794.31gold quality
dorsal root ganglionUBERON:000004494.29gold quality
subthalamic nucleusUBERON:000190694.24gold quality
substantia nigra pars compactaUBERON:000196594.17gold quality
body of tongueUBERON:001187694.15gold quality
substantia nigra pars reticulataUBERON:000196694.12gold quality
gingival epitheliumUBERON:000194993.98gold quality
superior vestibular nucleusUBERON:000722793.98gold quality
deciduaUBERON:000245093.87gold quality
gingivaUBERON:000182893.77gold quality
CA1 field of hippocampusUBERON:000388193.75gold quality
orbitofrontal cortexUBERON:000416793.75gold quality
islet of LangerhansUBERON:000000693.67gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

ExperimentMarker?Max mean expression
E-ANND-3yes8.14
E-MTAB-6379no51.75

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

115 targeting FAM98A, 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-3613-3P100.0076.367965
HSA-MIR-432-3P100.0067.86705
HSA-MIR-12118100.0065.881270
HSA-MIR-513A-5P100.0069.772465
HSA-MIR-118499.9968.191458
HSA-MIR-548C-3P99.9974.017587
HSA-MIR-4789-3P99.9970.752484
HSA-MIR-548P99.9872.253784
HSA-MIR-1213699.9872.815713
HSA-MIR-4482-3P99.9872.503147
HSA-MIR-103A-3P99.9869.141595
HSA-MIR-10799.9869.141595
HSA-MIR-3173-3P99.9866.491217
HSA-MIR-6891-5P99.9866.531372
HSA-MIR-27A-3P99.9872.132955
HSA-MIR-27B-3P99.9872.132955
HSA-MIR-998599.9872.112939
HSA-MIR-548AN99.9770.912817
HSA-MIR-3065-5P99.9771.563281
HSA-MIR-1250-3P99.9670.044038
HSA-MIR-570-3P99.9672.414910
HSA-MIR-1468-3P99.9672.743797
HSA-MIR-144-3P99.9473.982698
HSA-MIR-335-3P99.9373.364958
HSA-MIR-129799.9173.413162
HSA-MIR-10527-5P99.9172.283754
HSA-MIR-380-3P99.8970.181978
HSA-MIR-3140-3P99.8868.472069
HSA-MIR-30A-3P99.8769.742928
HSA-MIR-30D-3P99.8769.922917

Literature-anchored findings (GeneRIF, showing 4)

  • FAM98A is expressed in numerous ovarian cancer cell lines and is important for the malignant characteristics of ovarian cancer cells. (PMID:26503212)
  • the two structural homologs FAM98A and FAM98B included in a novel complex with DDX1 and C14orf166 are required for PRMT1 expression in colorectal cancer cell lines (PMID:28040436)
  • Mechanistically, it was demonstrated that miR-142-3p directly targeted FAM98A, and modulated its expression. (PMID:31114934)
  • Circular RNA intraflagellar transport 80 facilitates endometrial cancer progression through modulating miR-545-3p/FAM98A signaling. (PMID:34783205)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_reriofam98aENSDARG00000078391
mus_musculusFam98aENSMUSG00000002017
rattus_norvegicusFam98aENSRNOG00000030328
drosophila_melanogasterCG5913FBGN0039385
caenorhabditis_elegansWBGENE00044326

Paralogs (2): FAM98C (ENSG00000130244), FAM98B (ENSG00000171262)

Protein

Protein identifiers

Protein FAM98AQ8NCA5 (reviewed: Q8NCA5)

All UniProt accessions (9): A0A8I5KR56, A0A8I5KX90, A0A8I5KXK5, A0A8I5KZA5, Q8NCA5, A0A8I5QKV4, A0A8I5QKV5, B4DT23, E9PH82

UniProt curated annotations — full annotation on UniProt →

Function. Positively stimulates PRMT1-induced protein arginine methylation. Involved in skeletal homeostasis. Positively regulates lysosome peripheral distribution and ruffled border formation in osteoclasts.

Subunit / interactions. Interacts (via N- and C-terminus) with DDX1. Interacts (via N- and C-terminus) with C14orf166. Interacts with FAM98B. Interacts with PLEKHM1 (via N- and C-terminus).

Tissue specificity. Expressed strongly in colorectal cancer cells. Expressed strongly in colorectal cancer tissues compared to wild-type colon samples (at protein level). Expressed strongly in colorectal cancer tissues compared to wild-type colon samples.

Similarity. Belongs to the FAM98 family.

RefSeq proteins (2): NP_001291467, NP_056290* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR018797FAM98Family

Pfam: PF10239

UniProt features (13 total): compositionally biased region 8, region of interest 2, sequence conflict 2, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q8NCA5-F168.950.41

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 213 (showing top): MYOGENIN_Q6, TGCGCANK_UNKNOWN, BASSO_B_LYMPHOCYTE_NETWORK, GOBP_TRNA_METABOLIC_PROCESS, GOBP_REGULATION_OF_RUFFLE_ASSEMBLY, GOBP_REGULATION_OF_CELLULAR_COMPONENT_BIOGENESIS, CAGCTG_AP4_Q5, MONNIER_POSTRADIATION_TUMOR_ESCAPE_UP, GOBP_POSITIVE_REGULATION_OF_CELLULAR_COMPONENT_BIOGENESIS, GOBP_REGULATION_OF_CELL_PROJECTION_ORGANIZATION, DEURIG_T_CELL_PROLYMPHOCYTIC_LEUKEMIA_DN, MYOD_01, GOBP_RNA_SPLICING_VIA_ENDONUCLEOLYTIC_CLEAVAGE_AND_LIGATION, GOBP_RNA_SPLICING, OCT1_07

GO Biological Process (6): tRNA splicing, via endonucleolytic cleavage and ligation (GO:0006388), protein methylation (GO:0006479), positive regulation of cell population proliferation (GO:0008284), positive regulation of gene expression (GO:0010628), lysosome localization (GO:0032418), positive regulation of ruffle assembly (GO:1900029)

GO Molecular Function (3): RNA binding (GO:0003723), protein methyltransferase activity (GO:0008276), protein binding (GO:0005515)

GO Cellular Component (3): nucleus (GO:0005634), cytoplasm (GO:0005737), tRNA-splicing ligase complex (GO:0072669)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
RNA splicing, via endonucleolytic cleavage and ligation1
tRNA processing1
protein alkylation1
macromolecule methylation1
cell population proliferation1
regulation of cell population proliferation1
positive regulation of cellular process1
gene expression1
regulation of gene expression1
positive regulation of macromolecule biosynthetic process1
vacuolar localization1
ruffle assembly1
positive regulation of plasma membrane bounded cell projection assembly1
regulation of ruffle assembly1
nucleic acid binding1
methyltransferase activity1
catalytic activity, acting on a protein1
binding1
intracellular membrane-bounded organelle1
intracellular anatomical structure1
cellular anatomical structure1
intracellular protein-containing complex1
catalytic complex1

Protein interactions and networks

STRING

1052 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
FAM98ADDX1Q92499893
FAM98ARTCBQ9Y3I0729
FAM98ARTRAFQ9Y224727
FAM98AATXN2Q99700691
FAM98AHNRNPUL2Q1KMD3666
FAM98ADHX36Q9H2U1657
FAM98ANUFIP2Q7Z417647
FAM98ADHX15O43143640
FAM98AELAVL1Q15717621
FAM98AC2orf49Q9BVC5620
FAM98APRPF3O43395612
FAM98ANDEL1Q9GZM8592
FAM98AATXN2LQ8WWM7580
FAM98AELAVL4P26378569
FAM98AELAVL3Q14576569

IntAct

122 interactions, top by confidence:

ABTypeScore
GDI1RAB4Apsi-mi:“MI:0914”(association)0.820
FAM98ARTRAFpsi-mi:“MI:0915”(physical association)0.810
RTRAFFAM98Apsi-mi:“MI:0915”(physical association)0.810
FAM98ADDX1psi-mi:“MI:0915”(physical association)0.780
DDX1FAM98Apsi-mi:“MI:0915”(physical association)0.780
NSPIK3R2psi-mi:“MI:0914”(association)0.750
FAM98AHERC2psi-mi:“MI:0914”(association)0.640
FAM98ANUFIP2psi-mi:“MI:0914”(association)0.640
YWHAGBLTP3Bpsi-mi:“MI:0914”(association)0.640
YWHAHBLTP3Bpsi-mi:“MI:0914”(association)0.570
tatPPM1Gpsi-mi:“MI:0914”(association)0.560
RACGAP1CHEK1psi-mi:“MI:0914”(association)0.530
NRRP9psi-mi:“MI:0914”(association)0.530
NNOP56psi-mi:“MI:0914”(association)0.530
NRBM47psi-mi:“MI:0914”(association)0.530
FUSDDX3Xpsi-mi:“MI:0914”(association)0.430
FAM98AFAM98Bpsi-mi:“MI:0915”(physical association)0.400
FAM98AFAM98Apsi-mi:“MI:0915”(physical association)0.400
TK2psi-mi:“MI:0915”(physical association)0.400
SDC1ILVBLpsi-mi:“MI:0915”(physical association)0.400

BioGRID (312): FAM98A (Affinity Capture-MS), C14orf166 (Two-hybrid), FAM98A (Affinity Capture-RNA), FAM98A (Affinity Capture-MS), FAM98A (Affinity Capture-MS), FAM98A (Affinity Capture-MS), FAM98A (Affinity Capture-MS), C14orf166 (Co-fractionation), FAM98A (Co-fractionation), FAM98A (Co-fractionation), PFKM (Co-fractionation), FAM98A (Affinity Capture-MS), FAM98A (Affinity Capture-MS), FAM98A (Affinity Capture-MS), FAM98A (Affinity Capture-MS)

ESM2 similar proteins: A4IFB1, A6H7H1, A9ULY7, B1H1X4, B5DDX6, B5DF93, B5X165, D3Z8X7, O60308, P70501, Q05AW9, Q28HX4, Q3TC46, Q3TJZ6, Q52LJ0, Q5EA95, Q5FWT1, Q5R4R4, Q5R539, Q5R679, Q5R8Q4, Q5RHQ8, Q60520, Q62418, Q66I22, Q6A0A9, Q6DEZ2, Q6IVW0, Q80V31, Q80VD1, Q86TB9, Q8BH43, Q8BXG3, Q8CBY3, Q8CDG3, Q8CF97, Q8K2L8, Q8NCA5, Q8ND56, Q8R3P2

Diamond homologs: Q17RN3, Q3TJZ6, Q52LJ0, Q5FWT1, Q5R679, Q80VD1, Q8NCA5

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 122 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:

PathwayPartnersFoldFDR
SARS-CoV-1-host interactions714.8×2e-04
Nonsense-Mediated Decay (NMD)514.0×3e-03
Formation of the ternary complex, and subsequently, the 43S complex513.0×3e-03
Translation initiation complex formation511.5×3e-03
Ribosomal scanning and start codon recognition511.5×3e-03
SARS-CoV-1 Infection610.3×3e-03
rRNA processing in the nucleus and cytosol59.7×5e-03
Signaling by ALK fusions and activated point mutants59.1×5e-03

GO biological processes:

GO termPartnersFoldFDR
intrinsic apoptotic signaling pathway517.4×1e-03
negative regulation of translation713.3×4e-04
ribosomal small subunit biogenesis613.3×1e-03
cytoplasmic translation712.6×4e-04
positive regulation of translation511.1×6e-03
rRNA processing68.2×6e-03
translation77.0×6e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance81
Likely benign2
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

2270 predictions. Top by Δscore:

VariantEffectΔscore
2:33543508:GCA:Gacceptor_loss1.0000
2:33543509:CAGT:Cacceptor_loss1.0000
2:33543510:A:AGacceptor_gain1.0000
2:33543510:AGTC:Aacceptor_loss1.0000
2:33543510:AGTCT:Aacceptor_gain1.0000
2:33543511:G:GGacceptor_gain1.0000
2:33543511:GT:Gacceptor_gain1.0000
2:33543511:GTCT:Gacceptor_gain1.0000
2:33543511:GTCTG:Gacceptor_gain1.0000
2:33543623:GATCA:Gdonor_gain1.0000
2:33543624:A:Gdonor_gain1.0000
2:33543624:ATCA:Adonor_gain1.0000
2:33543625:TCA:Tdonor_gain1.0000
2:33543628:G:GGdonor_gain1.0000
2:33549747:GATTT:Gdonor_gain1.0000
2:33549748:ATTT:Adonor_gain1.0000
2:33549752:G:GGdonor_gain1.0000
2:33585693:TGGCT:Tacceptor_gain1.0000
2:33585694:GGCT:Gacceptor_gain1.0000
2:33585696:CT:Cacceptor_gain1.0000
2:33585698:C:CCacceptor_gain1.0000
2:33585701:T:TCacceptor_gain1.0000
2:33586557:TGTA:Tdonor_loss1.0000
2:33586558:GTACC:Gdonor_loss1.0000
2:33586559:TAC:Tdonor_loss1.0000
2:33586561:C:Adonor_loss1.0000
2:33586566:G:Cdonor_gain1.0000
2:33586677:TC:Tacceptor_gain1.0000
2:33586678:CC:Cacceptor_gain1.0000
2:33586679:C:CCacceptor_gain1.0000

AlphaMissense

3328 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
2:33585367:C:AW322C1.000
2:33585367:C:GW322C1.000
2:33585369:A:GW322R1.000
2:33585369:A:TW322R1.000
2:33585377:A:CM319R1.000
2:33585377:A:GM319T1.000
2:33585409:T:AR308S1.000
2:33585409:T:GR308S1.000
2:33585410:C:GR308T1.000
2:33585414:C:GG307R1.000
2:33585416:C:AG306V1.000
2:33585416:C:TG306D1.000
2:33585417:C:AG306C1.000
2:33585417:C:GG306R1.000
2:33585418:T:AR305S1.000
2:33585418:T:GR305S1.000
2:33585419:C:AR305I1.000
2:33585419:C:GR305T1.000
2:33585422:T:AD304V1.000
2:33585422:T:CD304G1.000
2:33585422:T:GD304A1.000
2:33585423:C:GD304H1.000
2:33585437:A:GM299T1.000
2:33586577:C:AW235C1.000
2:33586577:C:GW235C1.000
2:33586579:A:GW235R1.000
2:33586579:A:TW235R1.000
2:33586588:A:GS232P1.000
2:33586617:A:GL222P1.000
2:33585358:C:AR325S0.999

dbSNP variants (sampled 300 via entrez): RS1000251531 (2:33599649 C>T), RS1000498688 (2:33590242 A>C,G), RS1000700693 (2:33596150 CT>C,CTT), RS1000827508 (2:33597640 C>T), RS1001155098 (2:33597320 C>T), RS1001224851 (2:33587455 A>G), RS1001254744 (2:33594221 T>C), RS1001287152 (2:33594479 C>A,T), RS1001313528 (2:33593581 C>T), RS1001491796 (2:33599707 C>G), RS1001525949 (2:33598784 A>G), RS1001817969 (2:33599565 G>C), RS1002225387 (2:33588668 C>A,T), RS1002274978 (2:33592970 C>A,T), RS1002292909 (2:33593143 C>G,T)

Disease associations

OMIM: gene MIM:620904 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

9 associations (top):

StudyTraitp-value
GCST000390_1Hypertension (young onset)3.000000e-10
GCST003461_2IgG response to Plasmodium falciparum antigens (GLURP, MSP2 FC27, MSP2 3D7)8.000000e-06
GCST003803_1Response to antidepressants in depression2.000000e-07
GCST003812_5Non-response to antidepressants and depression2.000000e-06
GCST003876_3Gut microbiota (beta diversity)5.000000e-08
GCST004068_49Venous thromboembolism adjusted for sickle cell variant rs77121243-T9.000000e-07
GCST006304_3Irritable bowel syndrome2.000000e-06
GCST008765_2Perceived intensity of aspartame4.000000e-06
GCST009391_1298Metabolite levels5.000000e-06

EFO canonical traits (3, from GWAS)

EFO IDTrait name
EFO:0007812Plasmodium falciparum antigen IgG measurement
EFO:0007874gut microbiome measurement
EFO:0010549xanthosine measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
Valproic Acidaffects cotreatment, increases expression, affects expression7
bisphenol Adecreases expression2
sodium arseniteincreases activity, affects cotreatment, increases abundance, increases expression, decreases expression2
FR900359decreases phosphorylation1
tremortinincreases expression1
2,4,6-tribromophenoldecreases expression1
triphenyl phosphateaffects expression1
sodium arsenatedecreases expression1
trichostatin Aincreases expression1
beta-lapachoneincreases expression1
manganese chlorideaffects cotreatment, increases abundance, increases expression1
isobutyl alcoholincreases abundance, increases expression, affects cotreatment1
beta-methylcholineaffects expression1
di-n-butylphosphoric acidaffects expression1
pentabromodiphenyl etherincreases expression1
chloropicrindecreases expression1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, increases expression1
nutlin 3affects cotreatment, increases secretion1
ICG 001decreases expression1
bisphenol Bincreases expression1
2,2’,4,4’-tetrabromodiphenyl etherdecreases expression1
dorsomorphinaffects cotreatment, increases expression1
hexabrominated diphenyl ether 153decreases expression1
2-(1H-indazol-4-yl)-6-(4-methanesulfonylpiperazin-1-ylmethyl)-4-morpholin-4-ylthieno(3,2-d)pyrimidinedecreases expression, increases response to substance1
bisphenol AFincreases expression1
4-(4-((5-(4,5-dimethyl-2-nitrophenyl)-2-furanyl)methylene)-4,5-dihydro-3-methyl-5-oxo-1H-pyrazol-1-yl)benzoic aciddecreases expression1
Resveratrolaffects cotreatment, increases expression1
Sunitinibdecreases expression1
Arsenicincreases abundance, increases expression, affects cotreatment1
Benzeneincreases expression1

Cellosaurus cell lines

1 cell lines: 1 cancer cell line

First 10 cell lines (id-ordered, not curated):

CellosaurusNameCategorySex
CVCL_B1RWAbcam HeLa FAM98A KOCancer cell lineFemale

Clinical trials (associated diseases)

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