FLVCR1

gene
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Also known as FLVCRMFSD7BPCASLC49A1

Summary

FLVCR1 (FLVCR choline and heme transporter 1, HGNC:24682) is a protein-coding gene on chromosome 1q32.3, encoding Choline/ethanolamine transporter FLVCR1 (Q9Y5Y0). Uniporter that mediates the transport of extracellular choline and ethanolamine into cells, thereby playing a key role in phospholipid biosynthesis.

This gene encodes a member of the major facilitator superfamily of transporter proteins. The encoded protein is a heme transporter that may play a critical role in erythropoiesis by protecting developing erythroid cells from heme toxicity. This gene may play a role in posterior column ataxia with retinitis pigmentosa and the hematological disorder Diamond-Blackfan syndrome.

Source: NCBI Gene 28982 — RefSeq curated summary.

At a glance

  • Gene–disease (curated): FLVCR1-related retinopathy with or without ataxia (Definitive, ClinGen) — +1 more curated relationship
  • GWAS associations: 6
  • Clinical variants (ClinVar): 609 total — 34 pathogenic, 17 likely-pathogenic
  • Phenotypes (HPO): 113
  • MANE Select transcript: NM_014053

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:24682
Approved symbolFLVCR1
NameFLVCR choline and heme transporter 1
Location1q32.3
Locus typegene with protein product
StatusApproved
AliasesFLVCR, MFSD7B, PCA, SLC49A1
Ensembl geneENSG00000162769
Ensembl biotypeprotein_coding
OMIM609144
Entrez28982

Gene structure

Transcript identifiers

Ensembl transcripts: 9 — 6 protein_coding, 3 protein_coding_CDS_not_defined

ENST00000366971, ENST00000419102, ENST00000474693, ENST00000483790, ENST00000579295, ENST00000867613, ENST00000930967, ENST00000930968, ENST00000971333

RefSeq mRNA: 1 — MANE Select: NM_014053 NM_014053

CCDS: CCDS1510

Canonical transcript exons

ENST00000366971 — 10 exons

ExonStartEnd
ENSE00001068430212887891212888001
ENSE00001068434212863725212863869
ENSE00001443144212858275212859190
ENSE00001629822212895216212899363
ENSE00003529134212872678212872818
ENSE00003543077212888489212888594
ENSE00003559288212885293212885396
ENSE00003583473212889146212889257
ENSE00003596929212894986212895053
ENSE00003605605212883371212883438

Expression profiles

Bgee: expression breadth ubiquitous, 240 present calls, max score 98.88.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 8.7436 / max 327.2458, expressed in 1621 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter IDTPM avgSamples expressed
84916.76731516
84920.9927530
84900.9836569

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
jejunal mucosaUBERON:000039998.88gold quality
ileal mucosaUBERON:000033198.39gold quality
epithelial cell of pancreasCL:000008395.34gold quality
corpus epididymisUBERON:000435993.28gold quality
adrenal tissueUBERON:001830390.60gold quality
bronchial epithelial cellCL:000232890.46gold quality
buccal mucosa cellCL:000233689.88gold quality
duodenumUBERON:000211489.80gold quality
bronchusUBERON:000218589.52gold quality
germinal epithelium of ovaryUBERON:000130488.24gold quality
oviduct epitheliumUBERON:000480487.84gold quality
pylorusUBERON:000116687.21gold quality
pigmented layer of retinaUBERON:000178286.90gold quality
tibiaUBERON:000097986.87gold quality
trabecular bone tissueUBERON:000248386.77gold quality
pancreatic ductal cellCL:000207986.74gold quality
colonic mucosaUBERON:000031786.53gold quality
caput epididymisUBERON:000435886.21gold quality
seminal vesicleUBERON:000099886.15gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099186.10gold quality
calcaneal tendonUBERON:000370185.74gold quality
ventricular zoneUBERON:000305385.36gold quality
mucosa of sigmoid colonUBERON:000499385.27gold quality
visceral pleuraUBERON:000240184.78gold quality
islet of LangerhansUBERON:000000684.54gold quality
cerebellar vermisUBERON:000472084.51gold quality
jejunumUBERON:000211584.29gold quality
Brodmann (1909) area 23UBERON:001355483.57gold quality
sural nerveUBERON:001548883.27gold quality
bone marrow cellCL:000209283.05gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3yes4.54

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): EPAS1, ETS1

miRNA regulators (miRDB)

123 targeting FLVCR1, 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-6867-5P100.0082.213464
HSA-MIR-30A-5P100.0076.313233
HSA-MIR-30B-5P100.0076.293248
HSA-MIR-30C-5P100.0076.293248
HSA-MIR-30D-5P100.0076.323233
HSA-MIR-30E-5P100.0076.323242
HSA-MIR-1277-5P100.0073.955056
HSA-MIR-8485100.0077.574731
HSA-MIR-7110-3P100.0073.182486
HSA-MIR-6748-5P100.0065.811057
HSA-MIR-511-3P99.9968.851467
HSA-MIR-1213699.9872.815713
HSA-MIR-480399.9871.993117
HSA-MIR-477599.9875.006394
HSA-MIR-548P99.9872.253784
HSA-MIR-548N99.9871.944170
HSA-MIR-314899.9775.066478
HSA-MIR-548AN99.9770.912817
HSA-MIR-3065-5P99.9771.563281
HSA-MIR-1468-3P99.9672.743797
HSA-MIR-590-3P99.9674.346478
HSA-MIR-493-5P99.9672.472382
HSA-MIR-6778-3P99.9667.292693
HSA-MIR-365899.9673.874379
HSA-MIR-302E99.9670.742669
HSA-MIR-551B-5P99.9671.283493
HSA-MIR-6768-5P99.9267.361942
HSA-MIR-338-5P99.9272.342951
HSA-MIR-129799.9173.413162
HSA-MIR-10527-5P99.9172.283754

Literature-anchored findings (GeneRIF, showing 29)

  • the FLVCR gene on 1q31 is not involved in Diamond-Blackfan anemia in families studied (PMID:15996880)
  • results suggest that multiple FLVCR1 regions are critical for mediating efficient feline leukemia virus subgroup C (FeLV-C) infection and that these regions are distinct from the FeLV-C envelope binding site (PMID:16439531)
  • Alternative splicing of FLVCR1 transcripts and subsequent FLVCR1 insufficiency is an additional contributing factor to the erythropoietic defect observed in Diamond-Blackfan anemia. (PMID:18815190)
  • hemopexin directly interacts with FLVCR (PMID:20610401)
  • These results suggest that aberrant FLVCR1 causes a selective degeneration of a subpopulation of neurons in the retina and the posterior columns of the spinal cord via dysregulation of heme or iron homeostasis. (PMID:21070897)
  • Posterior column ataxia with retinitis pigmentosa is caused by mutations in FLVCR1. (PMID:21267618)
  • relative protein expression of 2 heme transporters, Feline Leukemia Virus, Subgroup C, Receptor 1 (FLVCR1) and Breast Cancer Resistance Protein, was assessed in placental tissue in relation to maternal/neonatal iron status and placental iron concentration (PMID:21593354)
  • Study identified sequence variants in the known disease-causing genes SLC6A3 and FLVCR1, and present evidence to strongly support the pathogenicity of variants identified in TUBGCP6, BRAT1, SNIP1, CRADD, and HARS. (PMID:22279524)
  • FLVCR1 mutants failed to fold properly in the ER, were rapidly degraded in the lysosomes, and therefore, could not export heme out of cells. Thus, accumulation of heme in FLVCR1-mutant cells could cause cellular toxicity. (PMID:22483575)
  • FLVCR1b regulates erythropoiesis by controlling mitochondrial heme efflux, whereas FLVCR1a expression is required to prevent hemorrhages and edema. (PMID:23187127)
  • both HIF2alpha and ETS1 are involved in the transcriptional regulation of Flvcr1a and that HIF2alpha is absolutely required for Flvcr1a induction upon hypoxia (PMID:24576667)
  • Flvcr1 regulates differentiation of erythroid progenitors by controlling intracellular heme accumulation. (PMID:25795718)
  • RPS19-downregulated erythroleukemia cells show reduced FLVCR1a and FLVCR1b mRNA levels associated with heme overload. (PMID:26058344)
  • Data shows that FLVCR1a participates in the control of intestinal mucosa homeostasis by exporting the excess of de novo synthesized heme from intestinal cells. (PMID:26067085)
  • Using fibroblasts and lymphoblastoid cell lines from patients with sensory neurodegeneration, we here show that the FLVCR1-mutations reduce heme export activity, enhance oxidative stress and increase sensitivity to programmed cell death. Our data link heme metabolism to sensory neuron maintenance and suggest that intracellular heme overload causes early-onset degeneration of pain-sensing neurons in humans (PMID:27923065)
  • Altogether, these findings showed a direct association between FLVCR1 mRNA levels and hyperglycemia, suggesting that increased adipose tissue heme exportation might disrupt, or is the consequence of, impaired systemic glucose metabolism during the progression to type 2 diabetes. (PMID:28706239)
  • Mutation in FLVCR1 gene is associated with Posterior column ataxia with retinitis pigmentosa coexisting with sensory-autonomic neuropathy and leukemia. (PMID:28766925)
  • Here, we describe a patient with non-syndromic retinitis pigmentosa homozygous for a splice-site variant in FLVCR1 (c.1092 + 5G>A) without evidence of posterior column ataxia or cerebellar degeneration. (PMID:29192808)
  • findings suggested that FLVCR1-AS1/miR-573/E2F3 axis was an important signaling pathway in mediating tumorigenesis and progression of NSCLC (PMID:30309647)
  • We describe clinical and retinal imaging features in the one of the largest cohorts of affected patients in the literature. Given the availability of genetic testing for this phenotype, testing for FLVCR1 mutations should be considered in pediatric and adult patients with sensory ataxia and retinitis pigmentosa. (PMID:30444160)
  • Mutations in FLVCR1 can present with the clinical picture of a non-syndromic autosomal recessive RP (in this case RP without PCA), RP with mild cerebellar signs, but also PCARP. (PMID:30656474)
  • FLVCR1 p.Tyr341Cys mutation was observed homozygously in seven Retinitis Pigmentosa affected Irish patients across four pedigrees. (PMID:31884612)
  • Isolated juvenile macular dystrophy without posterior column ataxia associated with FLVCR1 mutation. (PMID:34433355)
  • Extending the phenotype of posterior column ataxia with retinitis pigmentosa caused by variants in FLVCR1. (PMID:34931442)
  • Mfsd7b facilitates choline transport and missense mutations affect choline transport function. (PMID:38055060)
  • Structural basis of lipid head group entry to the Kennedy pathway by FLVCR1. (PMID:38693265)
  • Molecular mechanism of choline and ethanolamine transport in humans. (PMID:38778100)
  • Dysregulation of FLVCR1a-dependent mitochondrial calcium handling in neural progenitors causes congenital hydrocephalus. (PMID:39019006)
  • Apoptotic metabolites ameliorate bone aging phenotypes via TCOF1/FLVCR1-mediated mitochondrial homeostasis. (PMID:39237990)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_rerioflvcr1ENSDARG00000031587
mus_musculusFlvcr1ENSMUSG00000066595
rattus_norvegicusFlvcr1ENSRNOG00000049633
drosophila_melanogasterHisTFBGN0033196
caenorhabditis_elegansC09D4.1WBGENE00015632

Paralogs (4): FLVCR2 (ENSG00000119686), SLC49A4 (ENSG00000138463), SLC49A3 (ENSG00000169026), CFAP276 (ENSG00000179902)

Protein

Protein identifiers

Choline/ethanolamine transporter FLVCR1Q9Y5Y0 (reviewed: Q9Y5Y0)

Alternative names: Feline leukemia virus subgroup C receptor-related protein 1, Heme transporter FLVCR1

All UniProt accessions (2): Q9Y5Y0, H7C3Z2

UniProt curated annotations — full annotation on UniProt →

Function. Uniporter that mediates the transport of extracellular choline and ethanolamine into cells, thereby playing a key role in phospholipid biosynthesis. Choline and ethanolamine are the precursors of phosphatidylcholine and phosphatidylethanolamine, respectively, the two most abundant phospholipids. Transport is not coupled with proton transport and is exclusively driven by the choline (or ethanolamine) gradient across the plasma membrane. Also acts as a heme b transporter that mediates heme efflux from the cytoplasm to the extracellular compartment. Uniporter that mediates the transport of extracellular choline and ethanolamine into cells. Choline and ethanolamine are the precursors of phosphatidylcholine and phosphatidylethanolamine, respectively, the two most abundant phospholipids. Transport is not coupled with proton transport and is exclusively driven by the choline (or ethanolamine) gradient across the plasma membrane. Also acts as a heme b transporter that mediates heme efflux from the cytoplasm to the extracellular compartment. Heme export depends on the presence of HPX and is required to maintain intracellular free heme balance, protecting cells from heme toxicity. Heme export provides protection from heme or ferrous iron toxicities in liver, brain, sensory neurons and during erythropoiesis, a process in which heme synthesis intensifies. Possibly export coproporphyrin and protoporphyrin IX, which are both intermediate products in the heme biosynthetic pathway. Does not export bilirubin. The molecular mechanism of heme transport, whether electrogenic, electroneutral or coupled to other ions, remains to be elucidated. Heme b transporter that promotes heme efflux from the mitochondrion to the cytoplasm. Essential for erythroid differentiation. (Microbial infection) Confers susceptibility to feline leukemia virus subgroup C (FeLV-C) infection in vitro.

Subcellular location. Cell membrane Mitochondrion membrane.

Tissue specificity. Found all hematopoietic tissues including peripheral blood lymphocytes. Some expression is found in pancreas and kidney.

Post-translational modifications. N-Glycosylated.

Disease relevance. Retinopathy-sensory neuropathy syndrome (RETSNS) [MIM:609033] An autosomal recessive neurodegenerative syndrome beginning in infancy with areflexia and retinitis pigmentosa. Nyctalopia (night blindness) and peripheral visual field loss are usually evident during late childhood or teenage years, with subsequent progressive constriction of the visual fields and loss of central retinal function over time. A sensory ataxia caused by degeneration of the posterior columns of the spinal cord results in a loss of proprioceptive sensation that is clinically evident in the second decade of life and gradually progresses. Scoliosis, camptodactyly, achalasia, gastrointestinal dysmotility, and a sensory peripheral neuropathy are variable features of the disease. Affected individuals have no clinical or radiological evidence of cerebral or cerebellar involvement. Some patients have pain insensitivity and commonly manifest self-injury, ulcers and amputations. The disease is caused by variants affecting the gene represented in this entry. Defective neuronal heme transmembrane export due to FLVCR1 mutations may abrogate the neuroprotective effects of neuroglobin and initiate an apoptotic cascade that results in the selective degeneration of photoreceptors in the neurosensory retina and sensory neurons in the posterior spinal cord. Neurodevelopmental disorder with microcephaly, absent speech, and hypotonia (NEDMISH) [MIM:621060] A severe, autosomal recessive disorder characterized by profound global developmental delay, impaired intellectual development, absent speech, microcephaly, brain malformations, epilepsy, spasticity, and premature death. Brain malformations range from mild brain volume reduction to hydranencephaly. Additional features may include cortical visual impairment, sensory neuropathy, limb and digital malformations, and macrocytic anemia. The disease is caused by variants affecting the gene represented in this entry.

Miscellaneous. Has a probable mitochondrial transit peptide at positions 1-38.

Similarity. Belongs to the major facilitator superfamily. Feline leukemia virus subgroup C receptor (TC 2.A.1.28.1) family.

Isoforms (2)

UniProt IDNamesCanonical?
Q9Y5Y0-11, FLVCR1ayes
Q9Y5Y0-22, FLVCR1b, mitochondrial

RefSeq proteins (1): NP_054772* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR011701MFSFamily
IPR020846MFS_domDomain
IPR036259MFS_trans_sfHomologous_superfamily
IPR049680FLVCR1-2_SLC49-likeFamily

Pfam: PF07690

Catalyzed reactions (Rhea), 3 shown:

  • ethanolamine(in) = ethanolamine(out) (RHEA:32747)
  • choline(out) = choline(in) (RHEA:32751)
  • heme b(in) = heme b(out) (RHEA:75443)

UniProt features (86 total): sequence variant 22, helix 18, topological domain 13, transmembrane region 12, mutagenesis site 8, binding site 3, region of interest 2, modified residue 2, turn 2, chain 1, glycosylation site 1, splice variant 1, strand 1

Structure

Experimental structures (PDB)

8 structures.

PDBMethodResolution (Å)
8UC0ELECTRON MICROSCOPY2.42
8UBXELECTRON MICROSCOPY2.5
8UBWELECTRON MICROSCOPY2.59
8QCTELECTRON MICROSCOPY2.6
8UBYELECTRON MICROSCOPY2.67
8QCSELECTRON MICROSCOPY2.9
8R8TELECTRON MICROSCOPY2.9
8UBZELECTRON MICROSCOPY3.02

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9Y5Y0-F178.490.54

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Ligand- & substrate-binding residues (3): 214; 471; 471

Post-translational modifications (2): 56, 536

Glycosylation sites (1): 265

Mutagenesis-validated functional residues (8):

PositionPhenotype
125reduced transport of choline and ethanolamine.
151no effect on choline transmembrane transporter activity. no effect on ethanolamine transmembrane transporter activity.
153reduced transport of choline and ethanolamine.
214reduced transport of choline and nearly abolished transport of ethanolamine.
245slightly reduced transport of choline and ethanolamine.
349reduced transport of choline and ethanolamine.
443decreased choline and ethanolamine transmembrane transporter activity.
471slightly reduced transport of choline and ethanolamine.

Function

Pathways and Gene Ontology

Reactome pathways

2 pathways

IDPathway
R-HSA-189451Heme biosynthesis
R-HSA-917937Iron uptake and transport

MSigDB gene sets: 307 (showing top): GOBP_MYELOID_CELL_DIFFERENTIATION, GOBP_EMBRYO_DEVELOPMENT_ENDING_IN_BIRTH_OR_EGG_HATCHING, GOBP_PHOSPHOLIPID_METABOLIC_PROCESS, GOBP_BODY_MORPHOGENESIS, GOBP_MYELOID_CELL_HOMEOSTASIS, GOBP_SKELETAL_SYSTEM_DEVELOPMENT, GOBP_MYELOID_CELL_DEVELOPMENT, GOBP_IRON_COORDINATION_ENTITY_TRANSPORT, GOBP_EMBRYONIC_DIGIT_MORPHOGENESIS, GOBP_REGULATION_OF_DEVELOPMENTAL_GROWTH, GOBP_TRANSITION_METAL_ION_TRANSPORT, GOBP_EMBRYONIC_SKELETAL_SYSTEM_DEVELOPMENT, REACTOME_METABOLISM_OF_PORPHYRINS, GOBP_EMBRYONIC_SKELETAL_SYSTEM_MORPHOGENESIS, GOBP_ERYTHROCYTE_HOMEOSTASIS

GO Biological Process (20): blood vessel development (GO:0001568), in utero embryonic development (GO:0001701), heme biosynthetic process (GO:0006783), mitochondrial transport (GO:0006839), intracellular iron ion homeostasis (GO:0006879), phospholipid biosynthetic process (GO:0008654), choline transport (GO:0015871), heme transport (GO:0015886), erythrocyte differentiation (GO:0030218), multicellular organism growth (GO:0035264), embryonic digit morphogenesis (GO:0042733), erythrocyte maturation (GO:0043249), regulation of organ growth (GO:0046620), spleen development (GO:0048536), embryonic skeletal system morphogenesis (GO:0048704), head morphogenesis (GO:0060323), heme export (GO:0097037), ethanolamine transport (GO:0034229), limb morphogenesis (GO:0035108), transmembrane transport (GO:0055085)

GO Molecular Function (6): choline transmembrane transporter activity (GO:0015220), heme transmembrane transporter activity (GO:0015232), heme binding (GO:0020037), ethanolamine transmembrane transporter activity (GO:0034228), protein binding (GO:0005515), transmembrane transporter activity (GO:0022857)

GO Cellular Component (5): mitochondrion (GO:0005739), mitochondrial inner membrane (GO:0005743), plasma membrane (GO:0005886), membrane (GO:0016020), mitochondrial membrane (GO:0031966)

Reactome top-level categories

Rollup of top-2 pathways:

CategoryPathways
Metabolism of porphyrins1
Transport of small molecules1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
nitrogen compound transport2
heme transport2
transmembrane transporter activity2
vasculature development1
anatomical structure development1
chordate embryonic development1
porphyrin-containing compound biosynthetic process1
heme metabolic process1
pigment biosynthetic process1
intracellular transport1
intracellular monoatomic cation homeostasis1
inorganic ion homeostasis1
phospholipid metabolic process1
lipid biosynthetic process1
organophosphate biosynthetic process1
iron coordination entity transport1
myeloid cell differentiation1
erythrocyte homeostasis1
multicellular organismal process1
developmental growth1
embryonic limb morphogenesis1
embryonic morphogenesis1
cell maturation1
erythrocyte development1
organ growth1
regulation of developmental growth1
regulation of multicellular organismal process1
hematopoietic or lymphoid organ development1
embryonic organ morphogenesis1
skeletal system morphogenesis1
embryonic skeletal system development1
anatomical structure morphogenesis1
body morphogenesis1
head development1
amine transport1
organic hydroxy compound transport1
appendage morphogenesis1
limb development1
transport1
cellular process1

Protein interactions and networks

STRING

958 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
FLVCR1HPXP02790827
FLVCR1SLC48A1Q6P1K1724
FLVCR1SLC46A1Q96NT5717
FLVCR1ABCB10Q9NRK6649
FLVCR1STEAP3Q658P3617
FLVCR1FECHP22830615
FLVCR1ABCB6Q9NP58609
FLVCR1ALAS1P13196600
FLVCR1CPOXP36551578
FLVCR1SLC25A37Q9NYZ2578
FLVCR1SLC40A1Q9NP59571
FLVCR1PPOXP50336543
FLVCR1SLC11A2P49281541
FLVCR1ABCB7O75027529
FLVCR1CYBRD1Q53TN4527

IntAct

200 interactions, top by confidence:

ABTypeScore
CFTRESYT2psi-mi:“MI:2364”(proximity)0.710
IL2RGREEP6psi-mi:“MI:0914”(association)0.710
TMEM9BDNAJC13psi-mi:“MI:0914”(association)0.640
SLC20A1LIN7Apsi-mi:“MI:0914”(association)0.640
CD27TCAF2psi-mi:“MI:0914”(association)0.640
FAM234BABCD4psi-mi:“MI:0914”(association)0.620
SLC7A1TMEM223psi-mi:“MI:0914”(association)0.530
XKRXFAM234Bpsi-mi:“MI:0914”(association)0.530
ADGRG5KLRG2psi-mi:“MI:0914”(association)0.530
GYPBTCAF2psi-mi:“MI:0914”(association)0.530
TEX29TOR1Apsi-mi:“MI:0914”(association)0.530
NT5ESCAMP1psi-mi:“MI:0914”(association)0.530
SLC15A4PGRMC1psi-mi:“MI:0914”(association)0.530
TMEM9ESYT2psi-mi:“MI:0914”(association)0.530
VAMP5NBASpsi-mi:“MI:0914”(association)0.530
SLC22A9GPR89Apsi-mi:“MI:0914”(association)0.530
PTGIRTMEM63Apsi-mi:“MI:0914”(association)0.530
SLC22A16APBA3psi-mi:“MI:0914”(association)0.530
OPALINBTAF1psi-mi:“MI:0914”(association)0.530
ANKHFAM234Bpsi-mi:“MI:0914”(association)0.530
FLVCR1TNFRSF10Bpsi-mi:“MI:0914”(association)0.530
NRASESYT2psi-mi:“MI:2364”(proximity)0.480

BioGRID (190): FLVCR1 (Affinity Capture-MS), FLVCR1 (Affinity Capture-MS), FLVCR1 (Affinity Capture-MS), FLVCR1 (Affinity Capture-MS), FLVCR1 (Affinity Capture-MS), FLVCR1 (Affinity Capture-MS), FLVCR1 (Affinity Capture-MS), FLVCR1 (Affinity Capture-MS), FLVCR1 (Affinity Capture-MS), FLVCR1 (Proximity Label-MS), FLVCR1 (Proximity Label-MS), FLVCR1 (Affinity Capture-MS), FLVCR1 (Affinity Capture-MS), FLVCR1 (Affinity Capture-MS), FLVCR1 (Affinity Capture-MS)

ESM2 similar proteins: A0A0R4ILB2, A0A8M9Q308, A1A4N1, A2CER7, A5D7V7, A8WGF7, B0S5Y3, B2RXV4, B5X4H8, O00400, O00476, O01735, O23596, P30638, P36836, P46029, P60815, Q11073, Q16348, Q28722, Q28FF3, Q503P5, Q5F4B8, Q5RBM3, Q5XGK0, Q63424, Q6AYY8, Q6DDL7, Q6DIT7, Q6GMG6, Q6PB15, Q7Z3Q1, Q84XI3, Q86WB7, Q91X85, Q944P0, Q99808, Q99J27, Q9BZD2, Q9C8X2

Diamond homologs: A0A0R4ILB2, A0A8M9Q308, B2RXV4, O01735, P60815, Q91X85, Q9ES43, Q9N1F2, Q9UPI3, Q9Y5Y0, Q28FF3, Q501I9, Q66H95, Q6GNV7, Q8BFQ6, Q96SL1, Q11073, Q503P5, Q6UXD7, Q8CE47

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 175 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
Ras activation upon Ca2+ influx through NMDA receptor841.1×2e-09
Unblocking of NMDA receptors, glutamate binding and activation524.5×9e-05
Negative regulation of NMDA receptor-mediated neuronal transmission524.5×9e-05
Assembly and cell surface presentation of NMDA receptors1022.9×2e-09
Dopamine Neurotransmitter Release Cycle522.4×1e-04
Long-term potentiation521.4×1e-04
Neurotransmitter release cycle519.8×2e-04
Neurexins and neuroligins1119.5×2e-09

GO biological processes:

GO termPartnersFoldFDR
establishment or maintenance of epithelial cell apical/basal polarity1036.3×8e-11
protein localization to synapse628.7×9e-06
receptor clustering727.3×2e-06
regulation of postsynaptic membrane neurotransmitter receptor levels721.7×9e-06
cell-cell adhesion117.0×8e-05
exocytosis76.6×6e-03
protein-containing complex assembly96.4×1e-03
protein transport164.4×1e-04

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic34
Likely pathogenic17
Uncertain significance306
Likely benign155
Benign48

Top pathogenic / likely-pathogenic (30)

Variant IDHGVSClassification
1069108NM_014053.4(FLVCR1):c.1291dup (p.Thr431fs)Pathogenic
1069681NC_000001.10:g.(?213058615)(213058758_?)delPathogenic
1071648NM_014053.4(FLVCR1):c.1488dup (p.Leu497fs)Pathogenic
1377362NM_014053.4(FLVCR1):c.28del (p.Ala10fs)Pathogenic
1415512NM_014053.4(FLVCR1):c.561_656del (p.Ala188_Gly219del)Pathogenic
1451205NM_014053.4(FLVCR1):c.835del (p.Tyr279fs)Pathogenic
1456300NM_014053.4(FLVCR1):c.126del (p.Ala44fs)Pathogenic
1456369NC_000001.10:g.(?213061213)(213062619_?)delPathogenic
1457358NM_014053.4(FLVCR1):c.947del (p.Pro316fs)Pathogenic
18418NM_014053.4(FLVCR1):c.361A>G (p.Asn121Asp)Pathogenic
18419NM_014053.4(FLVCR1):c.721G>A (p.Ala241Thr)Pathogenic
1962180NM_014053.4(FLVCR1):c.154del (p.Ala52fs)Pathogenic
2007153NM_014053.4(FLVCR1):c.238del (p.Arg80fs)Pathogenic
2425886NC_000001.10:g.(?213046000)(213046180_?)delPathogenic
2425887NC_000001.10:g.(?213031795)(213037231_?)delPathogenic
2770146NM_014053.4(FLVCR1):c.1194C>A (p.Tyr398Ter)Pathogenic
3010005NM_014053.4(FLVCR1):c.1427del (p.Leu476fs)Pathogenic
30775NM_014053.4(FLVCR1):c.1477G>C (p.Gly493Arg)Pathogenic
3377003NM_014053.4(FLVCR1):c.441_445del (p.Trp148fs)Pathogenic
3383430NM_014053.4(FLVCR1):c.1193dup (p.Tyr398Ter)Pathogenic
3600271NM_014053.4(FLVCR1):c.610del (p.Met204fs)Pathogenic
3600274NM_014053.4(FLVCR1):c.1390G>A (p.Gly464Ser)Pathogenic
3600275NM_014053.4(FLVCR1):c.1328T>G (p.Leu443Arg)Pathogenic
3600279NM_014053.4(FLVCR1):c.382T>A (p.Tyr128Asn)Pathogenic
3721315NM_014053.4(FLVCR1):c.160dup (p.Arg54fs)Pathogenic
3725377NM_014053.4(FLVCR1):c.440_447del (p.Asp147fs)Pathogenic
379610NM_014053.4(FLVCR1):c.1093-1G>APathogenic
4074396NM_014053.4(FLVCR1):c.899dup (p.Arg301fs)Pathogenic
450232NM_014053.4(FLVCR1):c.1377dup (p.Gly460fs)Pathogenic
4730270NM_014053.4(FLVCR1):c.370C>T (p.Gln124Ter)Pathogenic

SpliceAI

2129 predictions. Top by Δscore:

VariantEffectΔscore
1:212872668:A:AGacceptor_gain1.0000
1:212872669:T:Gacceptor_gain1.0000
1:212872670:A:AGacceptor_gain1.0000
1:212872671:T:Gacceptor_gain1.0000
1:212872675:CA:Cacceptor_loss1.0000
1:212872676:A:AGacceptor_gain1.0000
1:212872677:G:GTacceptor_gain1.0000
1:212872677:GC:Gacceptor_gain1.0000
1:212872677:GCC:Gacceptor_gain1.0000
1:212872815:TATGG:Tdonor_loss1.0000
1:212872816:ATGGT:Adonor_loss1.0000
1:212872817:TGGTA:Tdonor_loss1.0000
1:212872819:G:GGdonor_gain1.0000
1:212872819:GT:Gdonor_loss1.0000
1:212872820:T:Gdonor_loss1.0000
1:212885397:G:GGdonor_gain1.0000
1:212887751:T:Aacceptor_gain1.0000
1:212895051:GCT:Gdonor_gain1.0000
1:212895054:G:GGdonor_gain1.0000
1:212895350:GAGAT:Gdonor_gain1.0000
1:212895352:GAT:Gdonor_gain1.0000
1:212863723:A:AGacceptor_gain0.9900
1:212863723:AGCTT:Aacceptor_gain0.9900
1:212863724:G:GGacceptor_gain0.9900
1:212863724:GCTTG:Gacceptor_gain0.9900
1:212864516:G:GTdonor_gain0.9900
1:212864517:A:Tdonor_gain0.9900
1:212870169:G:GGdonor_gain0.9900
1:212872663:C:CAacceptor_gain0.9900
1:212872665:T:TAacceptor_gain0.9900

AlphaMissense

3551 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
1:212859137:T:CF229L0.999
1:212859139:T:AF229L0.999
1:212859139:T:GF229L0.999
1:212863735:C:AA250E0.999
1:212858825:T:AW125R0.998
1:212858825:T:CW125R0.998
1:212859126:C:AA225D0.998
1:212859134:T:AW228R0.998
1:212859134:T:CW228R0.998
1:212859168:C:AA239D0.998
1:212863729:G:AG248E0.998
1:212863740:G:CG252R0.998
1:212863741:G:AG252D0.998
1:212883383:G:AG346D0.998
1:212885350:G:CG384R0.998
1:212885351:G:AG384D0.998
1:212889153:G:AG474E0.998
1:212859162:C:AA237D0.997
1:212863728:G:AG248R0.997
1:212863728:G:CG248R0.997
1:212863743:T:CF253L0.997
1:212863745:T:AF253L0.997
1:212863745:T:GF253L0.997
1:212883371:G:AG342D0.997
1:212883382:G:CG346R0.997
1:212885341:G:AG381R0.997
1:212885341:G:CG381R0.997
1:212885375:T:CL392P0.997
1:212888578:T:CL466P0.997
1:212889152:G:AG474R0.997

dbSNP variants (sampled 300 via entrez): RS1000082915 (1:212884406 A>G), RS1000330964 (1:212866110 A>G), RS1000485115 (1:212873036 A>G), RS1000543404 (1:212873200 C>T), RS1000663131 (1:212867572 G>A), RS1000726024 (1:212859490 G>A), RS1000814885 (1:212873326 GAAAGA>G), RS1000865057 (1:212884971 A>G), RS1000914773 (1:212873387 G>C), RS1000921427 (1:212878031 C>G), RS1000963358 (1:212860279 A>G), RS1001075184 (1:212859825 T>G), RS1001077425 (1:212897357 C>T), RS1001135817 (1:212870853 A>C,G), RS1001138006 (1:212896913 T>C)

Disease associations

OMIM: gene MIM:609144 | disease phenotypes: MIM:609033, MIM:268000, MIM:621060, MIM:208500, MIM:248200, MIM:162400

GenCC curated gene-disease

DiseaseClassificationInheritance
posterior column ataxia-retinitis pigmentosa syndromeDefinitiveAutosomal recessive
FLVCR1-related retinopathy with or without ataxiaStrongAutosomal recessive

ClinGen Gene-Disease Validity (1)

Expert-panel classifications — Definitive > Strong > Moderate > Limited > Disputed > Refuted.

DiseaseClassificationInheritance
FLVCR1-related retinopathy with or without ataxiaDefinitiveAR

Mondo (10): posterior column ataxia-retinitis pigmentosa syndrome (MONDO:0012177), retinitis pigmentosa (MONDO:0019200), neurodevelopmental disorder with microcephaly, absent speech, and hypotonia (MONDO:0976126), inherited retinal dystrophy (MONDO:0019118), sensory peripheral neuropathy (MONDO:0002321), Jeune syndrome (MONDO:0018770), short rib-polydactyly syndrome (MONDO:0015461), Stargardt disease (MONDO:0019353), hereditary sensory and autonomic neuropathy (MONDO:0015364), FLVCR1-related retinopathy with or without ataxia (MONDO:0100449)

Orphanet (7): Posterior column ataxia-retinitis pigmentosa syndrome (Orphanet:88628), Retinitis pigmentosa (Orphanet:791), OBSOLETE: Inherited retinal disorder (Orphanet:71862), Jeune syndrome (Orphanet:474), Short rib-polydactyly syndrome (Orphanet:1505), Stargardt disease (Orphanet:827), Hereditary sensory and autonomic neuropathy (Orphanet:140471)

HPO phenotypes

113 total (30 of 113 shown, HPO-id order):

HPOTerm
HP:0000007Autosomal recessive inheritance
HP:0000010Recurrent urinary tract infections
HP:0000011Neurogenic bladder
HP:0000020Urinary incontinence
HP:0000028Cryptorchidism
HP:0000104Renal agenesis
HP:0000105Enlarged kidney
HP:0000175Cleft palate
HP:0000218High palate
HP:0000238Hydrocephalus
HP:0000252Microcephaly
HP:0000272Malar flattening
HP:0000347Micrognathia
HP:0000369Low-set ears
HP:0000431Wide nasal bridge
HP:0000470Short neck
HP:0000510Rod-cone dystrophy
HP:0000518Cataract
HP:0000550Undetectable electroretinogram
HP:0000572Visual loss
HP:0000580Pigmentary retinopathy
HP:0000618Blindness
HP:0000648Optic atrophy
HP:0000662Nyctalopia
HP:0000729Autistic behavior
HP:0000742Self-mutilation
HP:0000763Sensory neuropathy
HP:0000821Hypothyroidism
HP:0000879Short sternum
HP:0001059Pterygium

GWAS associations

6 associations (top):

StudyTraitp-value
GCST007800_23Asthma (childhood onset)3.000000e-10
GCST010083_4Hemoglobin levels1.000000e-12
GCST90002383_347Hematocrit4.000000e-09
GCST90002384_25Hemoglobin7.000000e-10
GCST90002385_104High light scatter reticulocyte count1.000000e-10
GCST90002386_390High light scatter reticulocyte percentage of red cells5.000000e-09

EFO canonical traits (3, from GWAS)

EFO IDTrait name
EFO:0004509hemoglobin measurement
EFO:0004348hematocrit
EFO:0007986reticulocyte count

MeSH disease descriptors (7)

DescriptorNameTree numbers
D009477Hereditary Sensory and Autonomic NeuropathiesC10.500.250; C10.574.500.493; C10.668.829.800.175; C16.131.666.310; C16.320.400.415
D058499Retinal DystrophiesC11.768.585.658
D012174Retinitis PigmentosaC11.270.684; C11.768.585.658.500; C16.320.290.684
D012779Short Rib-Polydactyly SyndromeC05.116.099.708.857; C05.660.585.600.750; C16.131.077.850; C16.131.621.585.600.750
D000080362Stargardt DiseaseC11.270.872; C11.768.585.439.339; C16.320.290.724
C537571Jeune syndrome (supp.)
C536343Posterior column ataxia with retinitis pigmentosa (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

GtoPdb / IUPHAR curated pharmacology

(IUPHAR/BPS Guide to Pharmacology — expert-curated)

Target class: transporter — SLC49 family of FLVCR-related heme transporters

CTD chemical–gene interactions

26 total (human), top 26 by PubMed support.

ChemicalActions (top 5)PubMed papers
7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxidedecreases expression, increases expression3
FR900359decreases phosphorylation1
ethylbenzenedecreases expression, increases methylation, affects cotreatment1
alpha phellandrenedecreases expression1
triphenyl phosphateaffects expression1
sodium arsenitedecreases expression1
ICG 001decreases expression1
jinfukangdecreases expression1
Sunitinibincreases expression1
Air Pollutantsdecreases expression, increases abundance1
Air Pollutants, Occupationaldecreases expression, increases methylation1
Atrazineincreases expression1
Caffeinedecreases phosphorylation1
Doxorubicindecreases expression1
Leadaffects splicing1
Tobacco Smoke Pollutiondecreases expression1
Tolueneaffects cotreatment, decreases expression, increases methylation1
Valproic Acidincreases expression1
Xylenesdecreases expression, increases methylation, affects cotreatment1
Cyclosporinedecreases expression1
Aflatoxin B1decreases expression, increases methylation1
Aflatoxin M1decreases expression1
Copper Sulfatedecreases expression1
Lactic Acidincreases expression1
Vitamin K 3affects expression1
Particulate Matterdecreases expression, increases abundance1

Cellosaurus cell lines

4 cell lines: 4 cancer cell line

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

CellosaurusNameCategorySex
CVCL_D4FZHCT116-FLVCR1-KO-c10Cancer cell lineMale
CVCL_D4G0HCT116-FLVCR1-KO-c2Cancer cell lineMale
CVCL_SN77HAP1 FLVCR1 (-) 1Cancer cell lineMale
CVCL_SN78HAP1 FLVCR1 (-) 2Cancer cell lineMale

Clinical trials (associated diseases)

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

TrialPhaseStatusTitle
NCT00717080PHASE4COMPLETEDThe Role of Capsular Tension Ring (CTR) in Anterior Capsular Contraction
NCT00000114PHASE3COMPLETEDRandomized Trial of Vitamin A and Vitamin E Supplementation for Retinitis Pigmentosa
NCT00000116PHASE3COMPLETEDRandomized Trial of DHA for Retinitis Pigmentosa Patients Receiving Vitamin A
NCT00346333PHASE3COMPLETEDClinical Trial of Lutein for Patients With Retinitis Pigmentosa Receiving Vitamin A
NCT01786395PHASE3TERMINATEDPhase III Efficacy and Safety Clinical Study of UF-021 for Treatment of Retinitis Pigmentosa
NCT04224207PHASE3COMPLETEDManagement of Retinitis Pigmentosa by Mesenchymal Stem Cells by Wharton’s Jelly Derived Mesenchymal Stem Cells
NCT04636853PHASE3COMPLETEDCB-PRP in Retinitis Pigmentosa and Dry Age-related Macular Degeneration
NCT05537220PHASE3ACTIVE_NOT_RECRUITINGOral N-acetylcysteine for Retinitis Pigmentosa
NCT05800301PHASE3COMPLETEDManagement of Retinitis Pigmentosa Via Combination of Wharton’s Jelly-derived Mesenchymal Stem Cells and Magnovision
NCT05926583PHASE3ACTIVE_NOT_RECRUITINGA Study of AAV5-hRKp.RPGR for the Treatment of Japanese Participants With X-linked Retinitis Pigmentosa
NCT06388200PHASE3ACTIVE_NOT_RECRUITINGA Phase 3 Study Of OCU400 Gene Therapy for the Treatment Of Retinitis Pigmentosa
NCT07082855PHASE3NOT_YET_RECRUITINGA Multicenter, Randomized, Double-Blind, Controlled Clinical Study of Minocycline for the Treatment of Retinitis Pigmentosa
NCT07290530PHASE3NOT_YET_RECRUITING24-Month Trial of NPI-001 for the Preservation of Photoreceptors in Retinitis Pigmentosa Associated With Usher Syndrome
NCT00100230PHASE2COMPLETEDDHA and X-Linked Retinitis Pigmentosa
NCT00447980PHASE2COMPLETEDA Study of Encapsulated Cell Technology (ECT) Implant for Participants With Early Stage Retinitis Pigmentosa
NCT00447993PHASE2COMPLETEDA Study of Encapsulated Cell Technology (ECT) Implant for Patients With Late Stage Retinitis Pigmentosa
NCT01233609PHASE2COMPLETEDTrial of Oral Valproic Acid for Retinitis Pigmentosa
NCT01399515PHASE2COMPLETEDEfficacy and Safety of Oral Valproic Acid for Retinitis Pigmentosa
NCT01530659PHASE2COMPLETEDRetinal Imaging in CNTF -Releasing Encapsulated Cell Implant Treated Patients for Early-stage Retinitis Pigmentosa
NCT01560715PHASE2COMPLETEDAutologous Bone Marrow-Derived Stem Cells Transplantation For Retinitis Pigmentosa
NCT02609165PHASE2COMPLETEDNerve Growth Factor Eye Drops Treatment in Patients With Retinitis Pigmentosa and Cystoid Macular Edema
NCT02661711PHASE2COMPLETEDAflibercept for Macular Oedema With Underlying Retinitis Pigmentosa (AMOUR) Study
NCT02804360PHASE2UNKNOWNIntravitreal Dexamethasone Implant in Retinitis Pigmentosa-related Macular Edema- a Retrospective Study
NCT02837640PHASE2UNKNOWNStudying a Potential Protective Effect of L-Dopa on Retinitis Pigmentosa
NCT03073733PHASE2COMPLETEDSafety and Efficacy of Intravitreal Injection of Human Retinal Progenitor Cells in Adults With Retinitis Pigmentosa
NCT04068207PHASE2COMPLETEDMinocycline Treatment in Retinitis Pigmentosa
NCT04356716PHASE2COMPLETEDSildenafil for Treatment of Choroidal Ischemia
NCT04604899PHASE2COMPLETEDSafety of Repeat Intravitreal Injection of Human Retinal Progenitor Cells (jCell) in Adult Subjects With Retinitis Pigmentosa
NCT04763369PHASE2UNKNOWNInvestigation of Therapeutic Efficacy and Safety of UMSCs for the Management of Retinitis Pigmentosa (RP)
NCT04864496PHASE2UNKNOWNEffects of Treatment With N- Acetylcysteine on Visual Outcomes in Patients With Retinitis Pigmentosa
NCT04945772PHASE2COMPLETEDEfficacy and Safety of MCO-010 Optogenetic Therapy in Adults With Retinitis Pigmentosa [RESTORE]
NCT05085964PHASE2TERMINATEDAn Open-Label Extension Study to Evaluate Safety & Tolerability of QR-421a in Subjects With Retinitis Pigmentosa
NCT05392179PHASE2COMPLETEDA Study in Subjects With Retinitis Pigmentosa
NCT06627179PHASE2RECRUITINGStudy to Evaluate Ultevursen in Subjects With Retinitis Pigmentosa (RP) Due to Mutations in Exon 13 of the USH2A Gene
NCT06628947PHASE2RECRUITINGA Phase II Study of Intravitreal KIO-301 in Patients With Late-stage Retinitis Pigmentosa
NCT06912633PHASE2RECRUITINGSafety of a Single, Intravitreal Injection of 6.0M jCell (Famzeretcel) in Retinitis Pigmentosa (RP)
NCT00063765PHASE1COMPLETEDEvaluation of Safety of Ciliary Neurotrophic Factor Implants in the Eye
NCT00065455PHASE1COMPLETEDInvestigating the Effect of Vitamin A Supplementation on Retinitis Pigmentosa
NCT00458575PHASE1TERMINATEDA Study to Evaluate the Safety of CNTO 2476 in Patients With Advanced Retinitis Pigmentosa
NCT01068561PHASE1COMPLETEDAutologous Bone Marrow-Derived Stem Cells Transplantation For Retinitis Pigmentosa