VCF1 (VCP nuclear cofactor family member 1) - Rat Genome Database

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Gene: VCF1 (VCP nuclear cofactor family member 1) Homo sapiens
Analyze
Symbol: VCF1
Name: VCP nuclear cofactor family member 1
RGD ID: 1602856
HGNC Page HGNC:25918
Description: ASSOCIATED WITH congenital disorder of glycosylation type IIg; genetic disease; INTERACTS WITH acrolein; alpha-pinene; benzo[a]pyrene
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: FAM104A; family with sequence similarity 104 member A; family with sequence similarity 104, member A; FLJ14775; hypothetical protein LOC84923
RGD Orthologs
Mouse
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381773,207,353 - 73,232,394 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1773,207,353 - 73,236,753 (-)EnsemblGRCh38hg38GRCh38
GRCh371771,203,492 - 71,228,533 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361768,715,087 - 68,740,128 (-)NCBINCBI36Build 36hg18NCBI36
Celera1767,786,638 - 67,811,677 (-)NCBICelera
Cytogenetic Map17q25.1NCBI
HuRef1766,612,519 - 66,637,546 (-)NCBIHuRef
CHM1_11771,267,552 - 71,292,613 (-)NCBICHM1_1
T2T-CHM13v2.01774,097,081 - 74,122,120 (-)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
2. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:9417904   PMID:12477932   PMID:14702039   PMID:15489334   PMID:16344560   PMID:22658674   PMID:23443559   PMID:25416956   PMID:26186194   PMID:26389662   PMID:26496610   PMID:28514442  
PMID:29599191   PMID:32296183   PMID:32814053   PMID:33961781   PMID:36300783   PMID:37713320  


Genomics

Comparative Map Data
VCF1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381773,207,353 - 73,232,394 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1773,207,353 - 73,236,753 (-)EnsemblGRCh38hg38GRCh38
GRCh371771,203,492 - 71,228,533 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361768,715,087 - 68,740,128 (-)NCBINCBI36Build 36hg18NCBI36
Celera1767,786,638 - 67,811,677 (-)NCBICelera
Cytogenetic Map17q25.1NCBI
HuRef1766,612,519 - 66,637,546 (-)NCBIHuRef
CHM1_11771,267,552 - 71,292,613 (-)NCBICHM1_1
T2T-CHM13v2.01774,097,081 - 74,122,120 (-)NCBIT2T-CHM13v2.0
Vcf1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3911113,552,145 - 113,574,988 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl11113,552,145 - 113,574,981 (-)EnsemblGRCm39 Ensembl
GRCm3811113,661,319 - 113,684,189 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl11113,661,319 - 113,684,155 (-)EnsemblGRCm38mm10GRCm38
MGSCv3711113,522,633 - 113,545,465 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv3611113,477,410 - 113,500,122 (-)NCBIMGSCv36mm8
Celera11125,425,403 - 125,448,233 (-)NCBICelera
Cytogenetic Map11E2NCBI
cM Map1179.12NCBI
Vcf1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81099,206,549 - 99,227,471 (-)NCBIGRCr8
mRatBN7.21098,707,404 - 98,728,486 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1098,707,410 - 98,728,728 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx10103,759,394 - 103,780,179 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.010103,222,439 - 103,243,226 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01098,627,444 - 98,648,370 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.010102,179,478 - 102,200,488 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl10102,179,478 - 102,200,596 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.010101,859,026 - 101,879,783 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.410103,291,220 - 103,312,198 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera1097,314,417 - 97,335,336 (-)NCBICelera
Cytogenetic Map10q32.1NCBI
Vcf1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955553232,369 - 251,265 (-)EnsemblChiLan1.0
ChiLan1.0NW_004955553230,193 - 251,322 (-)NCBIChiLan1.0ChiLan1.0
VCF1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21989,224,750 - 89,250,385 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11794,049,621 - 94,075,317 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01767,135,340 - 67,160,999 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11772,590,802 - 72,615,989 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1772,590,802 - 72,615,989 (-)Ensemblpanpan1.1panPan2
VCF1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.196,948,612 - 6,966,741 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha97,570,207 - 7,588,318 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.097,621,129 - 7,639,616 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl97,621,466 - 7,639,602 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.197,661,551 - 7,680,032 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.097,764,441 - 7,782,934 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.097,825,215 - 7,843,943 (+)NCBIUU_Cfam_GSD_1.0
Vcf1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_0244056027,505,139 - 7,524,256 (+)NCBIHiC_Itri_2
SpeTri2.0NW_0049366551,002,956 - 1,021,491 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
VCF1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl127,727,796 - 7,749,240 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1127,727,736 - 7,747,084 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2128,008,199 - 8,027,525 (+)NCBISscrofa10.2Sscrofa10.2susScr3
VCF1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11648,404,267 - 48,427,455 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1648,404,352 - 48,425,279 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366607719,225,532 - 19,248,764 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Vcf1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248013,295,258 - 3,312,124 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in VCF1
51 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 17q24.3-25.3(chr17:69209079-83086677)x3 copy number gain See cases [RCV000052486] Chr17:69209079..83086677 [GRCh38]
Chr17:67205220..81044553 [GRCh37]
Chr17:64716815..78637842 [NCBI36]
Chr17:17q24.3-25.3		 pathogenic
GRCh38/hg38 17q23.2-25.3(chr17:36449220-83086677)x3 copy number gain Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000052483]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000052483]|See cases [RCV000052483] Chr17:36449220..83086677 [GRCh38]
Chr17:58617905..81044553 [GRCh37]
Chr17:55972687..78637842 [NCBI36]
Chr17:17q23.2-25.3		 pathogenic
NM_001100621.2(C17orf80):c.783C>T (p.Val261=) single nucleotide variant Malignant melanoma [RCV000063292] Chr17:73236265 [GRCh38]
Chr17:71232404 [GRCh37]
Chr17:68743999 [NCBI36]
Chr17:17q25.1		 not provided
GRCh38/hg38 17q23.1-25.1(chr17:36449220-75053130)x3 copy number gain See cases [RCV000137437] Chr17:36449220..75053130 [GRCh38]
Chr17:57595736..73049225 [GRCh37]
Chr17:54950518..70560820 [NCBI36]
Chr17:17q23.1-25.1		 pathogenic
GRCh38/hg38 17q25.1(chr17:73031361-73264388)x3 copy number gain See cases [RCV000141363] Chr17:73031361..73264388 [GRCh38]
Chr17:71027500..71260527 [GRCh37]
Chr17:68539095..68772122 [NCBI36]
Chr17:17q25.1		 uncertain significance
GRCh38/hg38 17q24.3-25.3(chr17:69916435-83102552)x3 copy number gain See cases [RCV000143342] Chr17:69916435..83102552 [GRCh38]
Chr17:67912576..81048189 [GRCh37]
Chr17:65424171..78653717 [NCBI36]
Chr17:17q24.3-25.3		 pathogenic
NM_001098832.2(VCF1):c.*1228G>A single nucleotide variant COG1 congenital disorder of glycosylation [RCV000283612]|not provided [RCV002285314] Chr17:73208301 [GRCh38]
Chr17:71204440 [GRCh37]
Chr17:17q25.1		 benign|likely benign|uncertain significance
NM_018714.3(COG1):c.2900C>G (p.Pro967Arg) single nucleotide variant COG1 congenital disorder of glycosylation [RCV000702152]|Inborn genetic diseases [RCV002523005] Chr17:73208408 [GRCh38]
Chr17:71204547 [GRCh37]
Chr17:17q25.1		 uncertain significance
NM_018714.3(COG1):c.2816dup (p.Ala940fs) duplication COG1 congenital disorder of glycosylation [RCV000778512]|not provided [RCV000730241] Chr17:73208318..73208319 [GRCh38]
Chr17:71204457..71204458 [GRCh37]
Chr17:17q25.1		 uncertain significance
GRCh37/hg19 17q24.2-25.3(chr17:64241326-81041938)x3 copy number gain See cases [RCV000447577] Chr17:64241326..81041938 [GRCh37]
Chr17:17q24.2-25.3		 pathogenic
GRCh37/hg19 17q21.31-25.3(chr17:42580684-81085615)x3 copy number gain See cases [RCV000447823] Chr17:42580684..81085615 [GRCh37]
Chr17:17q21.31-25.3		 pathogenic
GRCh37/hg19 17p13.3-q25.3(chr17:526-81041938) copy number gain See cases [RCV000511439] Chr17:526..81041938 [GRCh37]
Chr17:17p13.3-q25.3		 pathogenic
NM_001098832.2(VCF1):c.178A>T (p.Ser60Cys) single nucleotide variant Inborn genetic diseases [RCV003270023] Chr17:73232129 [GRCh38]
Chr17:71228268 [GRCh37]
Chr17:17q25.1		 uncertain significance
NM_001098832.2(VCF1):c.464A>C (p.Glu155Ala) single nucleotide variant Inborn genetic diseases [RCV003286574] Chr17:73209689 [GRCh38]
Chr17:71205828 [GRCh37]
Chr17:17q25.1		 uncertain significance
NM_001098832.2(VCF1):c.188C>T (p.Pro63Leu) single nucleotide variant Inborn genetic diseases [RCV003278013] Chr17:73232119 [GRCh38]
Chr17:71228258 [GRCh37]
Chr17:17q25.1		 uncertain significance
NM_018714.3(COG1):c.2836G>A (p.Asp946Asn) single nucleotide variant COG1 congenital disorder of glycosylation [RCV001046057]|not provided [RCV000514967] Chr17:73208344 [GRCh38]
Chr17:71204483 [GRCh37]
Chr17:17q25.1		 uncertain significance
GRCh37/hg19 17q24.2-25.3(chr17:67002415-81041938)x3 copy number gain See cases [RCV000512573] Chr17:67002415..81041938 [GRCh37]
Chr17:17q24.2-25.3		 pathogenic
GRCh37/hg19 17p13.3-q25.3(chr17:526-81041938)x3 copy number gain See cases [RCV000512441] Chr17:526..81041938 [GRCh37]
Chr17:17p13.3-q25.3		 pathogenic
GRCh37/hg19 17q24.1-25.3(chr17:63689671-81041938)x3 copy number gain not provided [RCV000683952] Chr17:63689671..81041938 [GRCh37]
Chr17:17q24.1-25.3		 pathogenic
GRCh37/hg19 17p13.3-q25.3(chr17:8547-81060040)x3 copy number gain not provided [RCV000739324] Chr17:8547..81060040 [GRCh37]
Chr17:17p13.3-q25.3		 pathogenic
GRCh37/hg19 17p13.3-q25.3(chr17:7214-81058310)x3 copy number gain not provided [RCV000739320] Chr17:7214..81058310 [GRCh37]
Chr17:17p13.3-q25.3		 pathogenic
GRCh37/hg19 17p13.3-q25.3(chr17:12344-81057996)x3 copy number gain not provided [RCV000739325] Chr17:12344..81057996 [GRCh37]
Chr17:17p13.3-q25.3		 pathogenic
GRCh37/hg19 17q24.1-25.2(chr17:64159738-74891024)x3 copy number gain not provided [RCV000762750] Chr17:64159738..74891024 [GRCh37]
Chr17:17q24.1-25.2		 likely pathogenic
NM_018714.3(COG1):c.2844A>G (p.Thr948=) single nucleotide variant COG1 congenital disorder of glycosylation [RCV002068657] Chr17:73208352 [GRCh38]
Chr17:71204491 [GRCh37]
Chr17:17q25.1		 likely benign
GRCh37/hg19 17q24.3-25.1(chr17:70720436-73175266) copy number gain not provided [RCV000767767] Chr17:70720436..73175266 [GRCh37]
Chr17:17q24.3-25.1		 pathogenic
NM_001098832.2(VCF1):c.*1219C>A single nucleotide variant not provided [RCV000898607] Chr17:73208310 [GRCh38]
Chr17:71204449 [GRCh37]
Chr17:17q25.1		 likely benign
NM_018714.3(COG1):c.2929A>G (p.Ser977Gly) single nucleotide variant COG1 congenital disorder of glycosylation [RCV000798657]|Inborn genetic diseases [RCV002537095] Chr17:73208437 [GRCh38]
Chr17:71204576 [GRCh37]
Chr17:17q25.1		 uncertain significance
GRCh37/hg19 17q24.1-25.3(chr17:62778720-81041938)x3 copy number gain not provided [RCV000849900] Chr17:62778720..81041938 [GRCh37]
Chr17:17q24.1-25.3		 pathogenic
NM_018714.3(COG1):c.2848C>T (p.Pro950Ser) single nucleotide variant COG1 congenital disorder of glycosylation [RCV001066712] Chr17:73208356 [GRCh38]
Chr17:71204495 [GRCh37]
Chr17:17q25.1		 uncertain significance
NM_001098832.2(VCF1):c.490G>A (p.Gly164Arg) single nucleotide variant Inborn genetic diseases [RCV003249703] Chr17:73209663 [GRCh38]
Chr17:71205802 [GRCh37]
Chr17:17q25.1		 uncertain significance
NM_001098832.2(VCF1):c.443C>T (p.Pro148Leu) single nucleotide variant Inborn genetic diseases [RCV003251624] Chr17:73209710 [GRCh38]
Chr17:71205849 [GRCh37]
Chr17:17q25.1		 uncertain significance
NM_018714.3(COG1):c.2822G>A (p.Arg941His) single nucleotide variant COG1 congenital disorder of glycosylation [RCV001242883] Chr17:73208330 [GRCh38]
Chr17:71204469 [GRCh37]
Chr17:17q25.1		 uncertain significance
NM_001098832.2(VCF1):c.*1037G>A single nucleotide variant COG1 congenital disorder of glycosylation [RCV001123811] Chr17:73208492 [GRCh38]
Chr17:71204631 [GRCh37]
Chr17:17q25.1		 uncertain significance
NM_018714.3(COG1):c.2826C>T (p.Ser942=) single nucleotide variant COG1 congenital disorder of glycosylation [RCV001493925] Chr17:73208334 [GRCh38]
Chr17:71204473 [GRCh37]
Chr17:17q25.1		 likely benign
NM_001098832.2(VCF1):c.*1385G>A single nucleotide variant not provided [RCV001541845] Chr17:73208144 [GRCh38]
Chr17:71204283 [GRCh37]
Chr17:17q25.1		 benign
NM_018714.3(COG1):c.2808T>C (p.Val936=) single nucleotide variant COG1 congenital disorder of glycosylation [RCV001123810] Chr17:73208316 [GRCh38]
Chr17:71204455 [GRCh37]
Chr17:17q25.1		 uncertain significance
NM_018714.3(COG1):c.2818G>A (p.Ala940Thr) single nucleotide variant COG1 congenital disorder of glycosylation [RCV001927605] Chr17:73208326 [GRCh38]
Chr17:71204465 [GRCh37]
Chr17:17q25.1		 uncertain significance
NM_018714.3(COG1):c.2866C>T (p.Gln956Ter) single nucleotide variant COG1 congenital disorder of glycosylation [RCV001961846] Chr17:73208374 [GRCh38]
Chr17:71204513 [GRCh37]
Chr17:17q25.1		 uncertain significance
NM_018714.3(COG1):c.2890A>G (p.Thr964Ala) single nucleotide variant COG1 congenital disorder of glycosylation [RCV001881032] Chr17:73208398 [GRCh38]
Chr17:71204537 [GRCh37]
Chr17:17q25.1		 uncertain significance
NM_018714.3(COG1):c.2867A>C (p.Gln956Pro) single nucleotide variant COG1 congenital disorder of glycosylation [RCV001990843] Chr17:73208375 [GRCh38]
Chr17:71204514 [GRCh37]
Chr17:17q25.1		 uncertain significance
NM_018714.3(COG1):c.2891C>T (p.Thr964Met) single nucleotide variant COG1 congenital disorder of glycosylation [RCV001938367] Chr17:73208399 [GRCh38]
Chr17:71204538 [GRCh37]
Chr17:17q25.1		 uncertain significance
NM_018714.3(COG1):c.2883A>C (p.Glu961Asp) single nucleotide variant COG1 congenital disorder of glycosylation [RCV001995821] Chr17:73208391 [GRCh38]
Chr17:71204530 [GRCh37]
Chr17:17q25.1		 uncertain significance
NM_018714.3(COG1):c.2840C>T (p.Pro947Leu) single nucleotide variant COG1 congenital disorder of glycosylation [RCV001907508] Chr17:73208348 [GRCh38]
Chr17:71204487 [GRCh37]
Chr17:17q25.1		 uncertain significance
NM_018714.3(COG1):c.2892G>A (p.Thr964=) single nucleotide variant COG1 congenital disorder of glycosylation [RCV002135769] Chr17:73208400 [GRCh38]
Chr17:71204539 [GRCh37]
Chr17:17q25.1		 likely benign
NM_018714.3(COG1):c.2841G>A (p.Pro947=) single nucleotide variant COG1 congenital disorder of glycosylation [RCV002204375] Chr17:73208349 [GRCh38]
Chr17:71204488 [GRCh37]
Chr17:17q25.1		 likely benign
NM_001098832.2(VCF1):c.11G>C (p.Arg4Pro) single nucleotide variant Inborn genetic diseases [RCV002687572] Chr17:73232296 [GRCh38]
Chr17:71228435 [GRCh37]
Chr17:17q25.1		 uncertain significance
NM_001098832.2(VCF1):c.62C>T (p.Ser21Leu) single nucleotide variant Inborn genetic diseases [RCV002969996] Chr17:73232245 [GRCh38]
Chr17:71228384 [GRCh37]
Chr17:17q25.1		 uncertain significance
NM_018714.3(COG1):c.2836G>C (p.Asp946His) single nucleotide variant Inborn genetic diseases [RCV002782818] Chr17:73208344 [GRCh38]
Chr17:71204483 [GRCh37]
Chr17:17q25.1		 uncertain significance
NM_001098832.2(VCF1):c.*1231_*1235del deletion COG1 congenital disorder of glycosylation [RCV002667965] Chr17:73208294..73208298 [GRCh38]
Chr17:71204433..71204437 [GRCh37]
Chr17:17q25.1		 uncertain significance
NM_001098832.2(VCF1):c.74C>T (p.Ala25Val) single nucleotide variant Inborn genetic diseases [RCV002892076] Chr17:73232233 [GRCh38]
Chr17:71228372 [GRCh37]
Chr17:17q25.1		 uncertain significance
NM_001098832.2(VCF1):c.322A>G (p.Thr108Ala) single nucleotide variant Inborn genetic diseases [RCV002915903] Chr17:73212740 [GRCh38]
Chr17:71208879 [GRCh37]
Chr17:17q25.1		 uncertain significance
NM_001098832.2(VCF1):c.143C>G (p.Pro48Arg) single nucleotide variant Inborn genetic diseases [RCV002956041] Chr17:73232164 [GRCh38]
Chr17:71228303 [GRCh37]
Chr17:17q25.1		 uncertain significance
NM_001098832.2(VCF1):c.46C>T (p.Pro16Ser) single nucleotide variant Inborn genetic diseases [RCV002764234] Chr17:73232261 [GRCh38]
Chr17:71228400 [GRCh37]
Chr17:17q25.1		 uncertain significance
NM_001098832.2(VCF1):c.49A>C (p.Thr17Pro) single nucleotide variant Inborn genetic diseases [RCV002930655] Chr17:73232258 [GRCh38]
Chr17:71228397 [GRCh37]
Chr17:17q25.1		 uncertain significance
NM_001098832.2(VCF1):c.517G>C (p.Val173Leu) single nucleotide variant Inborn genetic diseases [RCV002891991] Chr17:73209636 [GRCh38]
Chr17:71205775 [GRCh37]
Chr17:17q25.1		 uncertain significance
NM_018714.3(COG1):c.2872G>A (p.Val958Ile) single nucleotide variant COG1 congenital disorder of glycosylation [RCV002646604] Chr17:73208380 [GRCh38]
Chr17:71204519 [GRCh37]
Chr17:17q25.1		 uncertain significance
NM_001098832.2(VCF1):c.532G>A (p.Ala178Thr) single nucleotide variant Inborn genetic diseases [RCV002680163] Chr17:73209621 [GRCh38]
Chr17:71205760 [GRCh37]
Chr17:17q25.1		 uncertain significance
NM_001098832.2(VCF1):c.434T>G (p.Ile145Ser) single nucleotide variant Inborn genetic diseases [RCV003173191] Chr17:73209719 [GRCh38]
Chr17:71205858 [GRCh37]
Chr17:17q25.1		 uncertain significance
NM_001098832.2(VCF1):c.238G>A (p.Gly80Ser) single nucleotide variant Inborn genetic diseases [RCV003219555] Chr17:73227248 [GRCh38]
Chr17:71223387 [GRCh37]
Chr17:17q25.1		 uncertain significance
NM_018714.3(COG1):c.2928T>C (p.Ser976=) single nucleotide variant COG1 congenital disorder of glycosylation [RCV003873690] Chr17:73208436 [GRCh38]
Chr17:71204575 [GRCh37]
Chr17:17q25.1		 likely benign
GRCh37/hg19 17q24.3-25.1(chr17:69501527-71380722)x1 copy number loss not provided [RCV003483324] Chr17:69501527..71380722 [GRCh37]
Chr17:17q24.3-25.1		 pathogenic
NM_001098832.2(VCF1):c.*1825G>A single nucleotide variant not provided [RCV003413323] Chr17:73207704 [GRCh38]
Chr17:71203843 [GRCh37]
Chr17:17q25.1		 likely benign
NM_018714.3(COG1):c.2825C>T (p.Ser942Phe) single nucleotide variant COG1 congenital disorder of glycosylation [RCV003610112] Chr17:73208333 [GRCh38]
Chr17:71204472 [GRCh37]
Chr17:17q25.1		 uncertain significance
NM_018714.3(COG1):c.2817G>A (p.Pro939=) single nucleotide variant COG1 congenital disorder of glycosylation [RCV003609841] Chr17:73208325 [GRCh38]
Chr17:71204464 [GRCh37]
Chr17:17q25.1		 likely benign
NM_018714.3(COG1):c.2862C>T (p.Phe954=) single nucleotide variant COG1 congenital disorder of glycosylation [RCV003881119] Chr17:73208370 [GRCh38]
Chr17:71204509 [GRCh37]
Chr17:17q25.1		 likely benign
NM_018714.3(COG1):c.2864G>A (p.Arg955Lys) single nucleotide variant Inborn genetic diseases [RCV004444427] Chr17:73208372 [GRCh38]
Chr17:71204511 [GRCh37]
Chr17:17q25.1		 uncertain significance
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:3161
Count of miRNA genes:941
Interacting mature miRNAs:1116
Transcripts:ENST00000403627, ENST00000405159, ENST00000579872, ENST00000580032, ENST00000581110, ENST00000583024, ENST00000583178
Prediction methods:Microtar, Miranda, Pita, Rnahybrid, Targetscan
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.

Markers in Region
RH18160  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh371771,203,508 - 71,203,709UniSTSGRCh37
Build 361768,715,103 - 68,715,304RGDNCBI36
Celera1767,786,654 - 67,786,855RGD
Cytogenetic Map17q25.1UniSTS
HuRef1766,612,535 - 66,612,736UniSTS
RH46289  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh371771,207,436 - 71,207,589UniSTSGRCh37
Build 361768,719,031 - 68,719,184RGDNCBI36
Celera1767,790,582 - 67,790,735RGD
Cytogenetic Map17q25.1UniSTS
HuRef1766,616,462 - 66,616,615UniSTS
GeneMap99-GB4 RH Map17460.2UniSTS
A004R48  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh371771,203,605 - 71,203,769UniSTSGRCh37
Build 361768,715,200 - 68,715,364RGDNCBI36
Celera1767,786,751 - 67,786,915RGD
Cytogenetic Map17q25.1UniSTS
HuRef1766,612,632 - 66,612,796UniSTS
GeneMap99-GB4 RH Map17459.98UniSTS
RH66739  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh371771,221,770 - 71,221,930UniSTSGRCh37
Build 361768,733,365 - 68,733,525RGDNCBI36
Celera1767,804,914 - 67,805,074RGD
Cytogenetic Map17q25.1UniSTS
HuRef1766,630,788 - 66,630,948UniSTS
GeneMap99-GB4 RH Map17460.71UniSTS
NCBI RH Map17751.9UniSTS
G64273  
Human AssemblyChrPosition (strand)SourceJBrowse
Cytogenetic Map17q25.1UniSTS


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 visual system adipose tissue appendage entire extraembryonic component pharyngeal arch
High
Medium 2102 2054 1274 235 1783 111 3888 1226 2136 213 1420 1583 141 1 1182 2326 6 2
Low 337 936 452 389 168 354 469 970 1598 206 40 30 34 22 462
Below cutoff 1 1

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001098832 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_001289410 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_001289411 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_001289412 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_032837 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_024451008 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_047436947 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_054317581 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_054317582 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AC097641 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AI926103 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK027681 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK074755 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK304556 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC011054 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC025238 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BG773537 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BX537858 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BX648968 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH471099 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CP068261 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CQ783651 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CQ871274 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CQ871276 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  DB265439 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  HY026689 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  HY037907 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  U92989 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENST00000403627   ⟹   ENSP00000384648
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1773,207,353 - 73,232,367 (-)Ensembl
RefSeq Acc Id: ENST00000405159   ⟹   ENSP00000384832
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1773,207,365 - 73,232,394 (-)Ensembl
RefSeq Acc Id: ENST00000579872   ⟹   ENSP00000462806
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1773,209,575 - 73,227,700 (-)Ensembl
RefSeq Acc Id: ENST00000580032   ⟹   ENSP00000462781
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1773,209,508 - 73,227,748 (-)Ensembl
RefSeq Acc Id: ENST00000581110   ⟹   ENSP00000462840
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1773,209,566 - 73,232,394 (-)Ensembl
RefSeq Acc Id: ENST00000583024   ⟹   ENSP00000462507
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1773,209,605 - 73,232,320 (-)Ensembl
RefSeq Acc Id: ENST00000583178
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1773,209,488 - 73,236,753 (-)Ensembl
RefSeq Acc Id: NM_001098832   ⟹   NP_001092302
RefSeq Status: VALIDATED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381773,207,365 - 73,232,394 (-)NCBI
GRCh371771,203,492 - 71,228,533 (-)RGD
Build 361768,715,087 - 68,740,128 (-)NCBI Archive
Celera1767,786,638 - 67,811,677 (-)RGD
HuRef1766,612,519 - 66,637,546 (-)ENTREZGENE
CHM1_11771,267,552 - 71,292,613 (-)NCBI
T2T-CHM13v2.01774,097,093 - 74,122,120 (-)NCBI
Sequence:
RefSeq Acc Id: NM_001289410   ⟹   NP_001276339
RefSeq Status: VALIDATED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381773,207,353 - 73,232,394 (-)NCBI
HuRef1766,612,519 - 66,637,546 (-)NCBI
CHM1_11771,267,552 - 71,292,613 (-)NCBI
T2T-CHM13v2.01774,097,081 - 74,122,120 (-)NCBI
Sequence:
RefSeq Acc Id: NM_001289411   ⟹   NP_001276340
RefSeq Status: VALIDATED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381773,207,353 - 73,232,394 (-)NCBI
HuRef1766,612,519 - 66,637,546 (-)NCBI
CHM1_11771,267,552 - 71,292,613 (-)NCBI
T2T-CHM13v2.01774,097,081 - 74,122,120 (-)NCBI
Sequence:
RefSeq Acc Id: NM_001289412   ⟹   NP_001276341
RefSeq Status: VALIDATED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381773,207,365 - 73,227,713 (-)NCBI
HuRef1766,612,519 - 66,637,546 (-)NCBI
CHM1_11771,267,552 - 71,287,922 (-)NCBI
T2T-CHM13v2.01774,097,093 - 74,117,438 (-)NCBI
Sequence:
RefSeq Acc Id: NM_032837   ⟹   NP_116226
RefSeq Status: VALIDATED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381773,207,365 - 73,232,394 (-)NCBI
GRCh371771,203,492 - 71,228,533 (-)RGD
Build 361768,715,087 - 68,740,128 (-)NCBI Archive
Celera1767,786,638 - 67,811,677 (-)RGD
HuRef1766,612,519 - 66,637,546 (-)ENTREZGENE
CHM1_11771,267,552 - 71,292,613 (-)NCBI
T2T-CHM13v2.01774,097,093 - 74,122,120 (-)NCBI
Sequence:
RefSeq Acc Id: XM_024451008   ⟹   XP_024306776
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381773,207,353 - 73,229,616 (-)NCBI
Sequence:
RefSeq Acc Id: XM_047436947   ⟹   XP_047292903
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381773,207,353 - 73,229,617 (-)NCBI
RefSeq Acc Id: XM_054317581   ⟹   XP_054173556
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
T2T-CHM13v2.01774,097,081 - 74,119,341 (-)NCBI
RefSeq Acc Id: XM_054317582   ⟹   XP_054173557
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
T2T-CHM13v2.01774,097,081 - 74,119,342 (-)NCBI
Reference Protein Sequences
RefSeq Acc Id: NP_116226   ⟸   NM_032837
- Peptide Label: isoform 2
- UniProtKB: B4E339 (UniProtKB/Swiss-Prot),   Q969W3 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: NP_001092302   ⟸   NM_001098832
- Peptide Label: isoform 1
- UniProtKB: Q969W3 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: NP_001276339   ⟸   NM_001289410
- Peptide Label: isoform 3
- UniProtKB: J3KT76 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: NP_001276340   ⟸   NM_001289411
- Peptide Label: isoform 4
- UniProtKB: J3KSI9 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: NP_001276341   ⟸   NM_001289412
- Peptide Label: isoform 5
- UniProtKB: J3KT52 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_024306776   ⟸   XM_024451008
- Peptide Label: isoform X1
- UniProtKB: J3KT52 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSP00000462781   ⟸   ENST00000580032
RefSeq Acc Id: ENSP00000462840   ⟸   ENST00000581110
RefSeq Acc Id: ENSP00000462507   ⟸   ENST00000583024
RefSeq Acc Id: ENSP00000384648   ⟸   ENST00000403627
RefSeq Acc Id: ENSP00000384832   ⟸   ENST00000405159
RefSeq Acc Id: ENSP00000462806   ⟸   ENST00000579872
RefSeq Acc Id: XP_047292903   ⟸   XM_047436947
- Peptide Label: isoform X2
RefSeq Acc Id: XP_054173557   ⟸   XM_054317582
- Peptide Label: isoform X2
RefSeq Acc Id: XP_054173556   ⟸   XM_054317581
- Peptide Label: isoform X1

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q969W3-F1-model_v2 AlphaFold Q969W3 1-186 view protein structure

Promoters
RGD ID:6794130
Promoter ID:HG_KWN:27010
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:CD4+TCell,   CD4+TCell_12Hour,   CD4+TCell_2Hour,   HeLa_S3,   K562,   Lymphoblastoid,   NB4
Transcripts:NM_001098832,   NM_001100621,   NM_001100622,   NM_017941,   NM_032837,   UC010DFJ.1
Position:
Human AssemblyChrPosition (strand)Source
Build 361768,739,226 - 68,740,717 (-)MPROMDB
RGD ID:7236175
Promoter ID:EPDNEW_H23833
Type:initiation region
Name:FAM104A_1
Description:family with sequence similarity 104 member A
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_H23837  
Experiment Methods:Single-end sequencing.
Position:
Human AssemblyChrPosition (strand)Source
GRCh381773,232,279 - 73,232,339EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene HGNC:25918 AgrOrtholog
COSMIC VCF1 COSMIC
Ensembl Genes ENSG00000133193 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Transcript ENST00000403627 ENTREZGENE
  ENST00000403627.7 UniProtKB/Swiss-Prot
  ENST00000405159 ENTREZGENE
  ENST00000405159.8 UniProtKB/Swiss-Prot
  ENST00000579872 ENTREZGENE
  ENST00000579872.1 UniProtKB/TrEMBL
  ENST00000581110 ENTREZGENE
  ENST00000581110.1 UniProtKB/TrEMBL
  ENST00000583024 ENTREZGENE
  ENST00000583024.1 UniProtKB/TrEMBL
GTEx ENSG00000133193 GTEx
HGNC ID HGNC:25918 ENTREZGENE
Human Proteome Map VCF1 Human Proteome Map
InterPro FAM104 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report hsa:84923 UniProtKB/Swiss-Prot
NCBI Gene 84923 ENTREZGENE
PANTHER PROTEIN FAM104A UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PTHR34763 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam FAM104 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PharmGKB PA142671787 PharmGKB
UniProt B4E339 ENTREZGENE
  F104A_HUMAN UniProtKB/Swiss-Prot
  J3KSI9 ENTREZGENE, UniProtKB/TrEMBL
  J3KT52 ENTREZGENE, UniProtKB/TrEMBL
  J3KT76 ENTREZGENE, UniProtKB/TrEMBL
  Q969W3 ENTREZGENE
UniProt Secondary B4E339 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2023-08-07 VCF1  VCP nuclear cofactor family member 1  FAM104A  family with sequence similarity 104 member A  Symbol and/or name change 19259463 PROVISIONAL
2015-11-24 FAM104A  family with sequence similarity 104 member A    family with sequence similarity 104, member A  Symbol and/or name change 5135510 APPROVED