FAAP100

gene
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Also known as FLJ22175

Summary

FAAP100 (FA core complex associated protein 100, HGNC:26171) is a protein-coding gene on chromosome 17q25.3, encoding Fanconi anemia core complex-associated protein 100 (Q0VG06). Plays a role in Fanconi anemia-associated DNA damage response network. It is a selective cancer dependency (DepMap: 14.3% of cell lines).

FAAP100 is a component of the Fanconi anemia (FA; MIM 277650) core complex and is required for core complex stability and FANCD2 (see MIM 227646) monoubiquitination (Ling et al., 2007 [PubMed 17396147]).

Source: NCBI Gene 80233 — RefSeq curated summary.

At a glance

  • Clinical variants (ClinVar): 177 total — 3 pathogenic, 1 likely-pathogenic
  • Phenotypes (HPO): 159
  • Cancer dependency (DepMap): dependent in 14.3% of screened cell lines
  • MANE Select transcript: NM_025161

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:26171
Approved symbolFAAP100
NameFA core complex associated protein 100
Location17q25.3
Locus typegene with protein product
StatusApproved
AliasesFLJ22175
Ensembl geneENSG00000185504
Ensembl biotypeprotein_coding
OMIM611301
Entrez80233

Gene structure

Transcript identifiers

Ensembl transcripts: 11 — 9 protein_coding, 2 nonsense_mediated_decay

ENST00000327787, ENST00000425898, ENST00000443656, ENST00000536161, ENST00000541246, ENST00000544302, ENST00000545865, ENST00000899631, ENST00000899632, ENST00000959821, ENST00000959822

RefSeq mRNA: 1 — MANE Select: NM_025161 NM_025161

CCDS: CCDS32765

Canonical transcript exons

ENST00000327787 — 9 exons

ExonStartEnd
ENSE000023020918155216681552353
ENSE000034837348155024881551203
ENSE000034925348153989181540950
ENSE000035180468154920681549362
ENSE000035222758154690981547678
ENSE000035550538154574681545882
ENSE000035983368154130981541395
ENSE000036560538154400481544120
ENSE000036679958155192881552052

Expression profiles

Bgee: expression breadth ubiquitous, 199 present calls, max score 92.82.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 18.9533 / max 166.7885, expressed in 1798 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter IDTPM avgSamples expressed
16875812.77971781
1687594.34471680
1687601.7572782
1687570.071725

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
right hemisphere of cerebellumUBERON:001489092.82gold quality
cerebellar hemisphereUBERON:000224592.42gold quality
cerebellar cortexUBERON:000212992.29gold quality
apex of heartUBERON:000209890.63gold quality
granulocyteCL:000009490.32gold quality
cerebellumUBERON:000203790.12gold quality
spleenUBERON:000210688.99gold quality
right lobe of thyroid glandUBERON:000111988.81gold quality
body of pancreasUBERON:000115088.60gold quality
metanephros cortexUBERON:001053388.33gold quality
cortical plateUBERON:000534388.29gold quality
left lobe of thyroid glandUBERON:000112087.88gold quality
left uterine tubeUBERON:000130387.82gold quality
right uterine tubeUBERON:000130287.65gold quality
right ovaryUBERON:000211886.80gold quality
right lobe of liverUBERON:000111486.68gold quality
thyroid glandUBERON:000204686.59gold quality
lower esophagus mucosaUBERON:003583486.58gold quality
body of uterusUBERON:000985386.40gold quality
small intestine Peyer’s patchUBERON:000345486.21gold quality
adenohypophysisUBERON:000219686.12gold quality
left ovaryUBERON:000211985.88gold quality
body of stomachUBERON:000116185.80gold quality
endocervixUBERON:000045885.78gold quality
right coronary arteryUBERON:000162585.73gold quality
ascending aortaUBERON:000149685.71gold quality
thoracic aortaUBERON:000151585.71gold quality
mucosa of transverse colonUBERON:000499185.66gold quality
ectocervixUBERON:001224985.65gold quality
stromal cell of endometriumCL:000225585.61gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3yes3.55

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

23 targeting FAAP100, 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-4481100.0066.421669
HSA-MIR-4745-5P99.9865.951028
HSA-MIR-185-3P99.9567.011743
HSA-MIR-128-3P99.9571.172484
HSA-MIR-216A-3P99.9571.192505
HSA-MIR-218-5P99.9372.222103
HSA-MIR-430299.8967.941187
HSA-MIR-3681-3P99.8870.462254
HSA-MIR-3065-3P99.8770.251407
HSA-MIR-431999.7669.832586
HSA-MIR-453099.6966.471509
HSA-MIR-211399.5871.221521
HSA-MIR-542-3P99.3467.581270
HSA-MIR-4733-3P98.3565.20994
HSA-MIR-63497.7467.11818
HSA-MIR-1226-3P97.5166.321063
HSA-MIR-663B97.4062.91664
HSA-MIR-6772-3P97.0465.89784
HSA-MIR-129196.2865.891224
HSA-MIR-6775-3P95.7665.91982
HSA-MIR-797695.7565.671186
HSA-MIR-6851-3P95.7365.11688
HSA-MIR-120489.5065.56109

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 14.3% of screened cell lines.

Literature-anchored findings (GeneRIF, showing 1)

  • FAAP100 as a new critical component of the FA-BRCA DNA damage response network. (PMID:17396147)

Cross-species orthologs

3 orthologs

OrganismSymbolGene ID
danio_reriofaap100ENSDARG00000079457
mus_musculusFaap100ENSMUSG00000025384
rattus_norvegicusFaap100ENSRNOG00000036699

Protein

Protein identifiers

Fanconi anemia core complex-associated protein 100Q0VG06 (reviewed: Q0VG06)

Alternative names: Fanconi anemia-associated protein of 100 kDa

All UniProt accessions (7): Q0VG06, E7EVV8, F5GZS4, F5H095, F5H5G6, I3L2L9, J3KQD8

UniProt curated annotations — full annotation on UniProt →

Function. Plays a role in Fanconi anemia-associated DNA damage response network. Regulates FANCD2 monoubiquitination and the stability of the FA core complex. Induces chromosomal instability as well as hypersensitivity to DNA cross-linking agents, when repressed.

Subunit / interactions. Belongs to the multisubunit FA complex composed of FANCA, FANCB, FANCC, FANCE, FANCF, FANCG, FANCL/PHF9, FANCM, FAAP24 and FAAP100. Forms a subcomplex with FANCB and FANCL.

Subcellular location. Nucleus.

Disease relevance. Fanconi anemia, complementation group X (FANCX) [MIM:621258] A form of Fanconi anemia, a disorder affecting all bone marrow elements and resulting in anemia, leukopenia and thrombopenia. It is associated with cardiac, renal and limb malformations, dermal pigmentary changes, and a predisposition to the development of malignancies. At the cellular level it is associated with hypersensitivity to DNA-damaging agents, chromosomal instability (increased chromosome breakage) and defective DNA repair. FANCX is an autosomal recessive form characterized by multiple pregnancy losses and offspring presenting with severe developmental and hematologic abnormalities leading to death in utero or in early life. The disease is caused by variants affecting the gene represented in this entry.

Isoforms (3)

UniProt IDNamesCanonical?
Q0VG06-11, byes
Q0VG06-22
Q0VG06-33, a

RefSeq proteins (1): NP_079437* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR029251Faap100Family

Pfam: PF15146

UniProt features (11 total): sequence variant 4, splice variant 3, chain 1, region of interest 1, sequence conflict 1, modified residue 1

Structure

Experimental structures (PDB)

6 structures.

PDBMethodResolution (Å)
7KZPELECTRON MICROSCOPY3.1
7KZSELECTRON MICROSCOPY4.2
7KZTELECTRON MICROSCOPY4.2
7KZVELECTRON MICROSCOPY4.2
7KZQELECTRON MICROSCOPY4.3
7KZRELECTRON MICROSCOPY4.4

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q0VG06-F174.470.15

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 (1): 667

Function

Pathways and Gene Ontology

Reactome pathways

2 pathways

IDPathway
R-HSA-6783310Fanconi Anemia Pathway
R-HSA-9833482PKR-mediated signaling

MSigDB gene sets: 299 (showing top): PID_FANCONI_PATHWAY, GSE45365_HEALTHY_VS_MCMV_INFECTION_CD8_TCELL_IFNAR_KO_DN, TGGTGCT_MIR29A_MIR29B_MIR29C, REACTOME_CYTOKINE_SIGNALING_IN_IMMUNE_SYSTEM, CAGCTG_AP4_Q5, AML_Q6, GOBP_DNA_DAMAGE_RESPONSE, GOBP_INTERSTRAND_CROSS_LINK_REPAIR, REACTOME_FANCONI_ANEMIA_PATHWAY, REACTOME_DNA_REPAIR, NIKOLSKY_BREAST_CANCER_17Q21_Q25_AMPLICON, NERF_Q2, WANG_PROSTATE_CANCER_ANDROGEN_INDEPENDENT, GOCC_FANCONI_ANAEMIA_NUCLEAR_COMPLEX, GOBP_DNA_METABOLIC_PROCESS

GO Biological Process (3): interstrand cross-link repair (GO:0036297), DNA repair (GO:0006281), DNA damage response (GO:0006974)

GO Molecular Function (2): DNA binding (GO:0003677), protein binding (GO:0005515)

GO Cellular Component (5): chromatin (GO:0000785), nucleus (GO:0005634), nucleoplasm (GO:0005654), cytosol (GO:0005829), Fanconi anaemia nuclear complex (GO:0043240)

Reactome top-level categories

Rollup of top-2 pathways:

CategoryPathways
DNA Repair1
Antimicrobial mechanism of IFN-stimulated genes1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure3
DNA repair1
DNA metabolic process1
DNA damage response1
cellular response to stress1
nucleic acid binding1
binding1
chromosome1
intracellular membrane-bounded organelle1
nuclear lumen1
cytoplasm1
nuclear protein-containing complex1

Protein interactions and networks

STRING

1192 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
FAAP100FANCBQ8NB91999
FAAP100FANCLQ9NW38999
FAAP100FANCAO15360998
FAAP100FAAP24Q9BTP7998
FAAP100FANCFQ9NPI8997
FAAP100FANCGO15287997
FAAP100FANCEQ9HB96996
FAAP100FANCMQ8IYD8995
FAAP100FANCCQ00597995
FAAP100F6S8H2F6S8H2992
FAAP100CENPSQ8N2Z9956
FAAP100CENPXA8MT69950
FAAP100FANCD2Q9BXW9907
FAAP100UBE2TQ9NPD8875
FAAP100FANCIQ9NVI1820

IntAct

122 interactions, top by confidence:

ABTypeScore
FANCGFANCApsi-mi:“MI:0914”(association)0.960
FANCAFANCGpsi-mi:“MI:0914”(association)0.960
FANCAFANCGpsi-mi:“MI:0403”(colocalization)0.960
SGF29NDC80psi-mi:“MI:0914”(association)0.840
KRT31HGSpsi-mi:“MI:0914”(association)0.780
KRT34TXLNApsi-mi:“MI:0914”(association)0.670
FANCAFAAP100psi-mi:“MI:0914”(association)0.660
FANCAFAAP100psi-mi:“MI:0915”(physical association)0.660
FAAP100FANCBpsi-mi:“MI:0915”(physical association)0.560
CDK18UBL4Apsi-mi:“MI:0914”(association)0.530
GPHA2PLXNA2psi-mi:“MI:0914”(association)0.530
DEUP1HIP1psi-mi:“MI:0914”(association)0.530
TSKSRGPD8psi-mi:“MI:0914”(association)0.530
GGA1CLCN3psi-mi:“MI:0914”(association)0.530
UBE2TFAAP100psi-mi:“MI:0914”(association)0.530
GRK7HSP90AA1psi-mi:“MI:0914”(association)0.530
RASSF8CORO1Apsi-mi:“MI:0914”(association)0.530
SYNGAP1YWHAEpsi-mi:“MI:0914”(association)0.530
NHSL3NCK2psi-mi:“MI:0914”(association)0.530
SKA2VSIG8psi-mi:“MI:0914”(association)0.530
CYCSFAAP100psi-mi:“MI:0914”(association)0.530
LAGE3CTSApsi-mi:“MI:0914”(association)0.530
LURAP1TRIM24psi-mi:“MI:0914”(association)0.530
SGF29MATN2psi-mi:“MI:0914”(association)0.530

BioGRID (160): C17orf70 (Affinity Capture-MS), C17orf70 (Affinity Capture-Western), C17orf70 (Affinity Capture-Western), C17orf70 (Affinity Capture-MS), C17orf70 (Two-hybrid), C17orf70 (Affinity Capture-Western), FANCM (Affinity Capture-MS), BLM (Affinity Capture-MS), FANCA (Affinity Capture-MS), TOP3A (Affinity Capture-MS), FANCB (Affinity Capture-MS), RMI1 (Affinity Capture-MS), FANCC (Affinity Capture-MS), FANCG (Affinity Capture-MS), FANCE (Affinity Capture-MS)

ESM2 similar proteins: A0JN53, A2ACJ2, D2I4M3, D4ACE5, E9Q2M9, G3HQ82, O15360, O75161, P59240, Q0VG06, Q1T7C0, Q24JP3, Q3KNJ2, Q3U5Q7, Q3U6Q4, Q3UK37, Q3ZAU7, Q400C9, Q400G9, Q571B6, Q5F479, Q5SW28, Q5UE93, Q6AYI4, Q6PJG6, Q6ZS81, Q7Z412, Q8BGI5, Q8BVF9, Q8C0R7, Q8C3R1, Q8C3S2, Q8CC12, Q8CEC0, Q8IWY9, Q8IXR5, Q8TC57, Q8TE82, Q8TF30, Q8WXE1

Diamond homologs: A2ACJ2, Q0VG06

SIGNOR signaling

1 interactions.

AEffectBMechanism
FAAP100“form complex”“Fanconi anemia core complex”binding

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 160 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
Fanconi Anemia Pathway514.1×7e-03
Formation of the cornified envelope98.0×1e-03

GO biological processes:

GO termPartnersFoldFDR
morphogenesis of an epithelium717.3×6e-05
intermediate filament organization915.6×5e-06
epithelial cell differentiation810.1×4e-04

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic3
Likely pathogenic1
Uncertain significance146
Likely benign13
Benign2

Top pathogenic / likely-pathogenic (4)

Variant IDHGVSClassification
3910000NM_025161.6(FAAP100):c.1151_1161del (p.Glu384fs)Pathogenic
3910001NM_025161.6(FAAP100):c.2590C>T (p.Gln864Ter)Pathogenic
3910002NM_025161.6(FAAP100):c.1624A>C (p.Thr542Pro)Pathogenic
4531686NM_025161.6(FAAP100):c.2311-1G>ALikely pathogenic

SpliceAI

1968 predictions. Top by Δscore:

VariantEffectΔscore
17:81540951:C:CCacceptor_gain1.0000
17:81541306:CA:Cdonor_loss1.0000
17:81541307:A:ACdonor_gain1.0000
17:81541307:ACC:Adonor_loss1.0000
17:81541307:ACCT:Adonor_gain1.0000
17:81541308:C:CCdonor_gain1.0000
17:81541308:CCT:Cdonor_gain1.0000
17:81541308:CCTC:Cdonor_gain1.0000
17:81541391:ATCGT:Aacceptor_gain1.0000
17:81541392:TCGT:Tacceptor_gain1.0000
17:81541393:CGT:Cacceptor_gain1.0000
17:81541393:CGTC:Cacceptor_gain1.0000
17:81541394:GT:Gacceptor_gain1.0000
17:81541395:TCTG:Tacceptor_loss1.0000
17:81541396:C:CCacceptor_gain1.0000
17:81541396:C:CGacceptor_loss1.0000
17:81543999:CATA:Cdonor_loss1.0000
17:81544000:ATACC:Adonor_loss1.0000
17:81544001:TA:Tdonor_loss1.0000
17:81549201:CTCA:Cdonor_loss1.0000
17:81549203:CAC:Cdonor_loss1.0000
17:81549204:ACCT:Adonor_loss1.0000
17:81549205:CCT:Cdonor_gain1.0000
17:81549359:CCAC:Cacceptor_gain1.0000
17:81549360:CAC:Cacceptor_gain1.0000
17:81549360:CACC:Cacceptor_gain1.0000
17:81549364:T:Cacceptor_loss1.0000
17:81552164:A:ACdonor_gain1.0000
17:81552165:C:CCdonor_gain1.0000
17:81552182:T:TAdonor_gain1.0000

AlphaMissense

5626 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
17:81547461:A:GW541R0.994
17:81547461:A:TW541R0.994
17:81550751:C:AG248V0.992
17:81547603:G:CS493R0.990
17:81547603:G:TS493R0.990
17:81547605:T:GS493R0.990
17:81550819:G:CF225L0.986
17:81550819:G:TF225L0.986
17:81550821:A:GF225L0.986
17:81550411:G:CS361R0.984
17:81550411:G:TS361R0.984
17:81550413:T:GS361R0.984
17:81547459:C:AW541C0.983
17:81547459:C:GW541C0.983
17:81551095:G:CF133L0.983
17:81551095:G:TF133L0.983
17:81551097:A:GF133L0.983
17:81550807:A:CF229L0.982
17:81550807:A:TF229L0.982
17:81550809:A:GF229L0.982
17:81544058:G:CS791R0.980
17:81544058:G:TS791R0.980
17:81544060:T:GS791R0.980
17:81544071:A:GI787T0.980
17:81550751:C:TG248D0.980
17:81550745:A:GL250P0.979
17:81547625:A:GL486P0.978
17:81550649:A:TV282D0.977
17:81547489:G:CN531K0.975
17:81547489:G:TN531K0.975

dbSNP variants (sampled 300 via entrez): RS1000196594 (17:81541601 C>A), RS1000423652 (17:81545647 G>GCC), RS1000781854 (17:81554588 T>A,C), RS1000929161 (17:81540029 C>G,T), RS1001020692 (17:81548346 G>T), RS1001026999 (17:81544661 C>T), RS1001217800 (17:81546148 GGGACCT>G), RS1001398303 (17:81542140 C>T), RS1001414641 (17:81553373 G>A), RS1001742754 (17:81553767 A>G), RS1001764327 (17:81541872 T>C), RS1001949984 (17:81554848 C>A), RS1002153818 (17:81549748 A>C), RS1002303164 (17:81545326 G>A), RS1002357462 (17:81541235 C>A,G,T)

Disease associations

OMIM: gene MIM:611301 | disease phenotypes: MIM:621258

GenCC curated gene-disease

Mondo (1): fanconi anemia, complementation group 10 (MONDO:0979241)

Orphanet (0):

HPO phenotypes

159 total (30 of 159 shown, HPO-id order):

HPOTerm
HP:0000007Autosomal recessive inheritance
HP:0000010Recurrent urinary tract infections
HP:0000023Inguinal hernia
HP:0000027Azoospermia
HP:0000028Cryptorchidism
HP:0000035Abnormal testis morphology
HP:0000047Hypospadias
HP:0000062Ambiguous genitalia
HP:0000072Hydroureter
HP:0000079Abnormality of the urinary system
HP:0000083Renal insufficiency
HP:0000086Ectopic kidney
HP:0000122Unilateral renal agenesis
HP:0000130Abnormality of the uterus
HP:0000135Hypogonadism
HP:0000175Cleft palate
HP:0000218High palate
HP:0000238Hydrocephalus
HP:0000252Microcephaly
HP:0000268Dolichocephaly
HP:0000286Epicanthus
HP:0000316Hypertelorism
HP:0000324Facial asymmetry
HP:0000340Sloping forehead
HP:0000347Micrognathia
HP:0000364Hearing abnormality
HP:0000365Hearing impairment
HP:0000377Abnormal pinna morphology
HP:0000452Choanal stenosis
HP:0000453Choanal atresia

GWAS associations

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
Estradiolincreases expression2
Particulate Matterincreases abundance, affects cotreatment, increases expression, decreases expression2
aristolochic acid Idecreases expression1
GSK-J4decreases expression1
FR900359decreases phosphorylation1
dicrotophosincreases expression1
bisphenol Adecreases methylation1
sodium arseniteincreases expression1
cobaltous chloridedecreases expression1
zinc chromatedecreases expression, increases abundance1
1-hydroxypyrenedecreases expression1
di-n-butylphosphoric acidaffects expression1
chromium hexavalent iondecreases expression, increases abundance1
ICG 001increases expression1
jinfukangincreases expression1
4-(4-((5-(4,5-dimethyl-2-nitrophenyl)-2-furanyl)methylene)-4,5-dihydro-3-methyl-5-oxo-1H-pyrazol-1-yl)benzoic acidincreases expression1
Temozolomideincreases expression1
Air Pollutantsdecreases expression, increases abundance1
Air Pollutants, Occupationaldecreases expression1
Ethanolaffects cotreatment, increases abundance, increases expression1
Atrazinedecreases expression1
Benzo(a)pyreneincreases methylation1
Formaldehydedecreases expression1
Gasolineincreases abundance, increases expression, affects cotreatment1
Leadaffects methylation1
Polycyclic Aromatic Hydrocarbonsaffects cotreatment, increases abundance, increases expression1
Smokedecreases expression1
Tobacco Smoke Pollutiondecreases expression1
Tretinoindecreases expression1
Valproic Acidincreases methylation1

Cellosaurus cell lines

2 cell lines: 2 cancer cell line

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

CellosaurusNameCategorySex
CVCL_SG11HAP1 C17orf70 (-) 1Cancer cell lineMale
CVCL_SG12HAP1 C17orf70 (-) 2Cancer cell lineMale

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): fanconi anemia, complementation group 10