FAM88C (family with sequence similarity 88 member C) - Rat Genome Database

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Gene: FAM88C (family with sequence similarity 88 member C) Homo sapiens
Analyze
Symbol: FAM88C
Name: family with sequence similarity 88 member C
RGD ID: 16551556
HGNC Page HGNC:56159
Description:
Type: ncrna (Ensembl: lncRNA)
RefSeq Status: VALIDATED
Previously known as: AL590399.1; Lnc-PPRL; LOC102724238; uncharacterized LOC102724238
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38.p14 Ensembl - Human Genome Assembly GRCh38 Ensembl
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38962,374,481 - 62,376,870 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl962,374,128 - 62,376,836 (-)EnsemblGRCh38hg38GRCh38
GRCh37946,685,782 - 46,688,171 (-)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map9q13NCBI
T2T-CHM13v2.0978,268,926 - 78,271,315 (-)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


References
Additional References at PubMed
PMID:35304111  


Genomics


Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 9p24.3-q34.3(chr9:203861-138125937)x3 copy number gain See cases [RCV000141876] Chr9:203861..138125937 [GRCh38]
Chr9:203861..141020389 [GRCh37]
Chr9:193861..140140210 [NCBI36]
Chr9:9p24.3-q34.3		 pathogenic
GRCh38/hg38 9p24.3-q34.3(chr9:193412-138124524)x3 copy number gain See cases [RCV000138783] Chr9:193412..138124524 [GRCh38]
Chr9:204090..141018976 [GRCh37]
Chr9:194090..140138797 [NCBI36]
Chr9:9p24.3-q34.3		 pathogenic
GRCh38/hg38 9p24.3-q34.3(chr9:193412-138159073)x3 copy number gain See cases [RCV000138962] Chr9:193412..138159073 [GRCh38]
Chr9:204104..141053525 [GRCh37]
Chr9:194104..140173346 [NCBI36]
Chr9:9p24.3-q34.3		 pathogenic|conflicting data from submitters
GRCh38/hg38 9p21.1-q21.11(chr9:31426827-68257015)x3 copy number gain See cases [RCV000141663] Chr9:31426827..68257015 [GRCh38]
Chr9:31426825..68330127 [GRCh37]
Chr9:31416825..67819947 [NCBI36]
Chr9:9p21.1-q21.11		 pathogenic
GRCh38/hg38 9p24.3-q34.3(chr9:203862-138125937)x3 copy number gain See cases [RCV000143476] Chr9:203862..138125937 [GRCh38]
Chr9:203862..141020389 [GRCh37]
Chr9:193862..140140210 [NCBI36]
Chr9:9p24.3-q34.3		 pathogenic
GRCh38/hg38 9p24.3-q21.31(chr9:193412-79877816)x3 copy number gain See cases [RCV000143012] Chr9:193412..79877816 [GRCh38]
Chr9:204104..82492731 [GRCh37]
Chr9:194104..81682551 [NCBI36]
Chr9:9p24.3-q21.31		 pathogenic
GRCh38/hg38 9p24.3-q34.3(chr9:193412-138124532)x3 copy number gain See cases [RCV000053745] Chr9:193412..138124532 [GRCh38]
Chr9:204193..141018984 [GRCh37]
Chr9:194193..140138805 [NCBI36]
Chr9:9p24.3-q34.3		 pathogenic
GRCh38/hg38 9p24.3-q22.1(chr9:203861-88130444)x4 copy number gain See cases [RCV000141904] Chr9:203861..88130444 [GRCh38]
Chr9:203861..90745359 [GRCh37]
Chr9:193861..89935179 [NCBI36]
Chr9:9p24.3-q22.1		 pathogenic
GRCh38/hg38 9p24.3-q21.12(chr9:193412-70630731)x3 copy number gain See cases [RCV000136152] Chr9:193412..70630731 [GRCh38]
Chr9:220253..73245647 [GRCh37]
Chr9:210253..72435467 [NCBI36]
Chr9:9p24.3-q21.12		 pathogenic
GRCh38/hg38 9p24.3-q21.13(chr9:193412-74615913)x3 copy number gain See cases [RCV000135954] Chr9:193412..74615913 [GRCh38]
Chr9:204193..77230829 [GRCh37]
Chr9:194193..76420649 [NCBI36]
Chr9:9p24.3-q21.13		 pathogenic
GRCh38/hg38 9p24.3-q34.3(chr9:193412-138179445)x3 copy number gain See cases [RCV000148113] Chr9:193412..138179445 [GRCh38]
Chr9:204193..141073897 [GRCh37]
Chr9:194193..140193718 [NCBI36]
Chr9:9p24.3-q34.3		 pathogenic
GRCh38/hg38 9p24.3-q34.3(chr9:193412-138114463)x3 copy number gain See cases [RCV000053746] Chr9:193412..138114463 [GRCh38]
Chr9:214367..141008915 [GRCh37]
Chr9:204367..140128736 [NCBI36]
Chr9:9p24.3-q34.3		 pathogenic
GRCh38/hg38 9p24.3-q21.11(chr9:204104-67549861)x3 copy number gain See cases [RCV000139208] Chr9:204104..67549861 [GRCh38]
Chr9:204104..66516698 [GRCh37]
Chr9:194104..66256518 [NCBI36]
Chr9:9p24.3-q21.11		 pathogenic
GRCh38/hg38 9q12-21.11(chr9:61053889-67217006)x1 copy number loss See cases [RCV000141597] Chr9:61053889..67217006 [GRCh38]
Chr9:39140222..40940341 [GRCh37]
Chr9:39130222..40955573 [NCBI36]
Chr9:9q12-21.11		 benign
GRCh38/hg38 9p13.3-q21.11(chr9:41747162-67217006)x3 copy number gain See cases [RCV000137784] Chr9:41747162..67217006 [GRCh38]
Chr9:33333162..71534501 [GRCh37]
Chr9:33323162..70724321 [NCBI36]
Chr9:9p13.3-q21.11		 pathogenic
GRCh38/hg38 9p24.3-q21.11(chr9:204104-66233120)x4 copy number gain See cases [RCV000137888] Chr9:204104..66233120 [GRCh38]
Chr9:204104..47212321 [GRCh37]
Chr9:194104..47002141 [NCBI36]
Chr9:9p24.3-q21.11		 pathogenic|conflicting data from submitters
GRCh38/hg38 9p11.2-q34.3(chr9:193412-138159073)x3 copy number gain See cases [RCV000139207] Chr9:193412..138159073 [GRCh38]
Chr9:68420641..141053525 [GRCh37]
Chr9:67910461..140173346 [NCBI36]
Chr9:9p11.2-q34.3		 pathogenic
GRCh38/hg38 9p22.2-q21.11(chr9:18344605-68257015) copy number gain See cases [RCV000140448] Chr9:18344605..68257015 [GRCh38]
Chr9:18344603..68995221 [GRCh37]
Chr9:18334603..68285041 [NCBI36]
Chr9:9p22.2-q21.11		 pathogenic
GRCh38/hg38 9p24.3-q34.3(chr9:193412-138179445)x3 copy number gain See cases [RCV000050348] Chr9:193412..138179445 [GRCh38]
Chr9:204193..141073897 [GRCh37]
Chr9:194193..140193718 [NCBI36]
Chr9:9p24.3-q34.3		 pathogenic
GRCh38/hg38 9p24.3-q34.3(chr9:204193-138179445) copy number gain See cases [RCV000133791] Chr9:204193..138179445 [GRCh38]
Chr9:204193..141073897 [GRCh37]
Chr9:194193..140193718 [NCBI36]
Chr9:9p24.3-q34.3		 pathogenic
GRCh38/hg38 9p24.3-q21.11(chr9:13997-68401065)x3 copy number gain See cases [RCV000135344] Chr9:13997..68401065 [GRCh38]
Chr9:13997..71015981 [GRCh37]
Chr9:3997..70205801 [NCBI36]
Chr9:9p24.3-q21.11		 pathogenic
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:575
Count of miRNA genes:394
Interacting mature miRNAs:429
Transcripts:ENST00000377518, ENST00000412631, ENST00000429818, ENST00000430302
Prediction methods:Microtar, Miranda, Rnahybrid
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system sensory system adipose tissue appendage entire extraembryonic component
High
Medium 1 1 1 5 1 1 1 8 4
Low 139 1 133 70 345 73 277 51 121 259 236 309 7 5
Below cutoff 621 925 699 259 343 185 1741 543 1439 85 541 516 76 504 1124 4

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000377518
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl962,374,128 - 62,376,783 (-)Ensembl
RefSeq Acc Id: ENST00000412631
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl962,375,328 - 62,376,126 (-)Ensembl
RefSeq Acc Id: ENST00000429818
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl962,374,462 - 62,376,780 (-)Ensembl
RefSeq Acc Id: ENST00000430302
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl962,375,332 - 62,376,836 (-)Ensembl
RefSeq Acc Id: NR_126048
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38962,374,481 - 62,376,870 (-)NCBI
T2T-CHM13v2.0978,268,926 - 78,271,315 (-)NCBI
Sequence:
Protein Sequences
GenBank Protein BAF82912 (Get FASTA)   NCBI Sequence Viewer  
  BAF85331 (Get FASTA)   NCBI Sequence Viewer  
Reference Protein Sequences


Additional Information

Database Acc Id Source(s)
COSMIC FAM88C COSMIC
Ensembl Genes ENSG00000204802 Ensembl, ENTREZGENE
Ensembl Transcript ENST00000377518 ENTREZGENE
GTEx ENSG00000204802 GTEx
HGNC ID HGNC:56159 ENTREZGENE
Human Proteome Map FAM88C Human Proteome Map
NCBI Gene LOC102724238 ENTREZGENE
RNAcentral URS0000BC45C9 RNACentral


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2022-01-17 FAM88C  family with sequence similarity 88 member C  AL590399.1  novel transcript  Symbol and/or name change 19259463 PROVISIONAL
2020-06-25 AL590399.1  novel transcript  LOC102724238  uncharacterized LOC102724238  Symbol and/or name change 19259462 PROVISIONAL
2020-06-18 LOC102724238  uncharacterized LOC102724238  AL590399.1  novel transcript  Symbol and/or name change 5135510 APPROVED