TMEM199 (transmembrane protein 199) - Rat Genome Database

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Gene: TMEM199 (transmembrane protein 199) Homo sapiens
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Symbol: TMEM199
Name: transmembrane protein 199
RGD ID: 1348837
HGNC Page HGNC:18085
Description: Predicted to enable oxysterol binding activity. Involved in cellular response to increased oxygen levels; intracellular monoatomic cation homeostasis; and lysosomal protein catabolic process. Located in COPI-coated vesicle membrane; endoplasmic reticulum; and endoplasmic reticulum-Golgi intermediate compartment membrane. Part of vacuolar proton-transporting V-type ATPase complex. Implicated in congenital disorder of glycosylation type IIp.
Type: protein-coding
RefSeq Status: REVIEWED
Previously known as: C17orf32; CDG2P; MGC45714; VMA12; VPH2
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
GRCh381728,357,647 - 28,363,683 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1728,357,642 - 28,363,683 (+)EnsemblGRCh38hg38GRCh38
GRCh371726,684,670 - 26,690,705 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361723,708,814 - 23,713,216 (+)NCBINCBI36Build 36hg18NCBI36
Build 341723,708,813 - 23,713,215NCBI
Celera1723,546,441 - 23,550,846 (+)NCBICelera
Cytogenetic Map17q11.2NCBI
HuRef1722,893,092 - 22,897,497 (+)NCBIHuRef
CHM1_11726,747,616 - 26,752,021 (+)NCBICHM1_1
T2T-CHM13v2.01729,299,496 - 29,305,534 (+)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease 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:8125298   PMID:12477932   PMID:15489334   PMID:21873635   PMID:24623722   PMID:25080503   PMID:25416956   PMID:25468996   PMID:26186194   PMID:26496610   PMID:26638075   PMID:26833330  
PMID:28296633   PMID:28298427   PMID:28514442   PMID:28692057   PMID:29117863   PMID:29395067   PMID:29509190   PMID:29568061   PMID:30194290   PMID:30639242   PMID:31056421   PMID:31091453  
PMID:31177093   PMID:31732153   PMID:31871319   PMID:32296183   PMID:32393512   PMID:32788342   PMID:32877691   PMID:33263384   PMID:33845483   PMID:33957083   PMID:33961781   PMID:34079125  
PMID:34186245   PMID:34349018   PMID:34373451   PMID:34626841   PMID:34709727   PMID:35271311   PMID:36610398   PMID:36706865   PMID:37223481   PMID:37774976   PMID:37931956   PMID:38117590  


Genomics

Comparative Map Data
TMEM199
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381728,357,647 - 28,363,683 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1728,357,642 - 28,363,683 (+)EnsemblGRCh38hg38GRCh38
GRCh371726,684,670 - 26,690,705 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361723,708,814 - 23,713,216 (+)NCBINCBI36Build 36hg18NCBI36
Build 341723,708,813 - 23,713,215NCBI
Celera1723,546,441 - 23,550,846 (+)NCBICelera
Cytogenetic Map17q11.2NCBI
HuRef1722,893,092 - 22,897,497 (+)NCBIHuRef
CHM1_11726,747,616 - 26,752,021 (+)NCBICHM1_1
T2T-CHM13v2.01729,299,496 - 29,305,534 (+)NCBIT2T-CHM13v2.0
Tmem199
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391178,397,881 - 78,402,994 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1178,397,881 - 78,402,998 (-)EnsemblGRCm39 Ensembl
GRCm381178,507,055 - 78,512,168 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1178,507,055 - 78,512,172 (-)EnsemblGRCm38mm10GRCm38
MGSCv371178,320,557 - 78,325,670 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361178,323,253 - 78,328,363 (-)NCBIMGSCv36mm8
Celera1188,139,128 - 88,144,241 (-)NCBICelera
Cytogenetic Map11B5NCBI
cM Map1146.74NCBI
Tmem199
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81063,900,543 - 63,905,115 (-)NCBIGRCr8
mRatBN7.21063,402,493 - 63,407,065 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1063,402,494 - 63,407,108 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1068,035,140 - 68,039,707 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01067,540,471 - 67,545,038 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01063,009,993 - 63,014,565 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01065,775,721 - 65,780,293 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1065,775,715 - 65,780,349 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01065,863,327 - 65,867,899 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41064,617,003 - 64,621,575 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera1062,379,068 - 62,383,640 (-)NCBICelera
Cytogenetic Map10q25NCBI
Tmem199
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554814,772,401 - 4,776,524 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554814,772,394 - 4,776,524 (-)NCBIChiLan1.0ChiLan1.0
TMEM199
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21936,096,421 - 36,101,069 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11737,976,799 - 37,981,439 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01728,412,229 - 28,416,840 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11728,914,604 - 28,919,194 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1728,914,604 - 28,919,194 (-)Ensemblpanpan1.1panPan2
TMEM199
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1942,607,688 - 42,614,776 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl942,607,733 - 42,611,445 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha941,764,608 - 41,771,703 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0943,426,851 - 43,433,952 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl943,426,891 - 43,434,130 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1942,211,085 - 42,218,182 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0942,502,309 - 42,509,401 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0942,579,367 - 42,586,467 (+)NCBIUU_Cfam_GSD_1.0
Tmem199
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440560241,634,919 - 41,639,459 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365384,511,941 - 4,517,498 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365384,512,866 - 4,517,404 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
TMEM199
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1244,636,379 - 44,641,527 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11244,636,379 - 44,641,536 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21246,548,851 - 46,554,004 (+)NCBISscrofa10.2Sscrofa10.2susScr3
TMEM199
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1 Ensembl1622,124,413 - 22,130,922 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_0236660757,998,384 - 8,004,370 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Tmem199
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_004624786961,890 - 966,430 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_004624786961,888 - 965,911 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in TMEM199
72 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 17q11.2(chr17:28283125-28904397)x3 copy number gain See cases [RCV000136494] Chr17:28283125..28904397 [GRCh38]
Chr17:26610151..27231415 [GRCh37]
Chr17:23634278..24255541 [NCBI36]
Chr17:17q11.2
benign
NM_152464.3(TMEM199):c.40G>C (p.Ala14Pro) single nucleotide variant TMEM199-CDG [RCV000208624] Chr17:28357710 [GRCh38]
Chr17:26684733 [GRCh37]
Chr17:17q11.2
pathogenic
NM_152464.3(TMEM199):c.376-1G>A single nucleotide variant TMEM199-CDG [RCV000208655] Chr17:28360528 [GRCh38]
Chr17:26687551 [GRCh37]
Chr17:17q11.2
pathogenic|likely benign
NM_152464.3(TMEM199):c.20C>A (p.Ala7Glu) single nucleotide variant Congenital disorders of glycosylation type II [RCV000210814]|TMEM199-CDG [RCV000208686]|not provided [RCV001268228] Chr17:28357690 [GRCh38]
Chr17:26684713 [GRCh37]
Chr17:17q11.2
pathogenic|likely pathogenic
NM_152464.3(TMEM199):c.92G>C (p.Arg31Pro) single nucleotide variant Congenital disorders of glycosylation type II [RCV000210790]|TMEM199-CDG [RCV000208697]|TMEM199-related disorder [RCV003407721]|not provided [RCV002517364] Chr17:28357762 [GRCh38]
Chr17:26684785 [GRCh37]
Chr17:17q11.2
pathogenic|likely pathogenic
GRCh37/hg19 17q11.1-11.2(chr17:25403446-31685464)x3 copy number gain not provided [RCV000762776] Chr17:25403446..31685464 [GRCh37]
Chr17:17q11.1-11.2
likely 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
GRCh37/hg19 17q11.1-11.2(chr17:25248166-30645676)x1 copy number loss Mitogen-activated protein kinase kinase inhibitor response [RCV000626439] Chr17:25248166..30645676 [GRCh37]
Chr17:17q11.1-11.2
drug response
NM_152464.3(TMEM199):c.256T>C (p.Tyr86His) single nucleotide variant not provided [RCV000514416] Chr17:28358960 [GRCh38]
Chr17:26685983 [GRCh37]
Chr17:17q11.2
benign|likely benign
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 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 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 17p11.2-q11.2(chr17:21279289-27474974)x2 copy number gain not provided [RCV000739439] Chr17:21279289..27474974 [GRCh37]
Chr17:17p11.2-q11.2
likely pathogenic
GRCh37/hg19 17q11.2(chr17:26619789-26723666)x1 copy number loss not provided [RCV000751972] Chr17:26619789..26723666 [GRCh37]
Chr17:17q11.2
uncertain significance
NM_152464.3(TMEM199):c.36G>A (p.Val12=) single nucleotide variant TMEM199-related disorder [RCV003895643]|not provided [RCV000928280] Chr17:28357706 [GRCh38]
Chr17:26684729 [GRCh37]
Chr17:17q11.2
likely benign|conflicting interpretations of pathogenicity
NM_152464.3(TMEM199):c.472G>A (p.Val158Ile) single nucleotide variant TMEM199-related disorder [RCV004731068]|not provided [RCV000965374] Chr17:28360788 [GRCh38]
Chr17:26687811 [GRCh37]
Chr17:17q11.2
benign
NM_152464.3(TMEM199):c.156A>G (p.Gln52=) single nucleotide variant TMEM199-CDG [RCV002502951]|not provided [RCV000953725] Chr17:28357826 [GRCh38]
Chr17:26684849 [GRCh37]
Chr17:17q11.2
benign|likely benign
NM_152464.3(TMEM199):c.496C>G (p.Leu166Val) single nucleotide variant not provided [RCV000831390] Chr17:28360812 [GRCh38]
Chr17:26687835 [GRCh37]
Chr17:17q11.2
benign
NM_152464.3(TMEM199):c.414G>A (p.Lys138=) single nucleotide variant not provided [RCV000937883] Chr17:28360567 [GRCh38]
Chr17:26687590 [GRCh37]
Chr17:17q11.2
likely benign
GRCh37/hg19 17p11.2-q21.2(chr17:21690653-38772647)x3 copy number gain not provided [RCV000846852] Chr17:21690653..38772647 [GRCh37]
Chr17:17p11.2-q21.2
pathogenic
NC_000017.11:g.28357366dup duplication not provided [RCV001655030] Chr17:28357364..28357365 [GRCh38]
Chr17:26684392 [GRCh37]
Chr17:17q11.2
benign
NM_152464.3(TMEM199):c.532-114C>T single nucleotide variant not provided [RCV001560310] Chr17:28361043 [GRCh38]
Chr17:26688065 [GRCh37]
Chr17:17q11.2
likely benign
NM_152464.3(TMEM199):c.286-120C>T single nucleotide variant not provided [RCV001684594] Chr17:28359195 [GRCh38]
Chr17:26686218 [GRCh37]
Chr17:17q11.2
benign
NC_000017.11:g.28357368T>G single nucleotide variant not provided [RCV001639505] Chr17:28357368 [GRCh38]
Chr17:26684394 [GRCh37]
Chr17:17q11.2
benign
NM_152464.3(TMEM199):c.375+233dup duplication not provided [RCV001658502] Chr17:28359636..28359637 [GRCh38]
Chr17:26686659..26686660 [GRCh37]
Chr17:17q11.2
benign
NM_152464.3(TMEM199):c.138T>C (p.Asp46=) single nucleotide variant not provided [RCV000917061] Chr17:28357808 [GRCh38]
Chr17:26684831 [GRCh37]
Chr17:17q11.2
likely benign
NM_152464.3(TMEM199):c.450C>T (p.Ile150=) single nucleotide variant not provided [RCV000885316] Chr17:28360766 [GRCh38]
Chr17:26687789 [GRCh37]
Chr17:17q11.2
likely benign
NM_152464.3(TMEM199):c.211+10A>C single nucleotide variant not provided [RCV000929506] Chr17:28357891 [GRCh38]
Chr17:26684914 [GRCh37]
Chr17:17q11.2
likely benign
NM_152464.3(TMEM199):c.375+8C>T single nucleotide variant not provided [RCV000913669] Chr17:28359412 [GRCh38]
Chr17:26686435 [GRCh37]
Chr17:17q11.2
likely benign
NM_152464.3(TMEM199):c.211+1G>A single nucleotide variant not provided [RCV002967496] Chr17:28357882 [GRCh38]
Chr17:26684905 [GRCh37]
Chr17:17q11.2
likely pathogenic
NC_000017.11:g.28357424= single nucleotide variant not provided [RCV001682198] Chr17:28357424 [GRCh38]
Chr17:26684449 [GRCh37]
Chr17:17q11.2
benign
NM_152464.3(TMEM199):c.531+32dup duplication not provided [RCV001689330] Chr17:28360875..28360876 [GRCh38]
Chr17:26687898..26687899 [GRCh37]
Chr17:17q11.2
benign
NC_000017.11:g.28357259del deletion not provided [RCV001635887] Chr17:28357258 [GRCh38]
Chr17:26684284 [GRCh37]
Chr17:17q11.2
benign
NM_152464.3(TMEM199):c.*207T>C single nucleotide variant not provided [RCV001590340] Chr17:28361459 [GRCh38]
Chr17:26688481 [GRCh37]
Chr17:17q11.2
likely benign
NM_152464.3(TMEM199):c.364G>A (p.Val122Ile) single nucleotide variant not provided [RCV001613822] Chr17:28359393 [GRCh38]
Chr17:26686416 [GRCh37]
Chr17:17q11.2
benign
NM_152464.3(TMEM199):c.376-66dup duplication not provided [RCV001696423] Chr17:28360461..28360462 [GRCh38]
Chr17:26687484..26687485 [GRCh37]
Chr17:17q11.2
benign
GRCh37/hg19 17q11.1-11.2(chr17:25274363-28450707)x3 copy number gain not provided [RCV001006886] Chr17:25274363..28450707 [GRCh37]
Chr17:17q11.1-11.2
pathogenic
NM_152464.3(TMEM199):c.375+18A>G single nucleotide variant not provided [RCV001538743] Chr17:28359422 [GRCh38]
Chr17:28359422..28359423 [GRCh38]
Chr17:26686445 [GRCh37]
Chr17:26686445..26686446 [GRCh37]
Chr17:17q11.2
benign
NM_152464.3(TMEM199):c.610G>T (p.Glu204Ter) single nucleotide variant TMEM199-CDG [RCV001337013] Chr17:28361235 [GRCh38]
Chr17:26688257 [GRCh37]
Chr17:17q11.2
pathogenic
NM_152464.3(TMEM199):c.28C>T (p.Arg10Ter) single nucleotide variant TMEM199-CDG [RCV001337012] Chr17:28357698 [GRCh38]
Chr17:26684721 [GRCh37]
Chr17:17q11.2
pathogenic
NC_000017.11:g.28357506_28357507dup duplication not provided [RCV001698908] Chr17:28357504..28357505 [GRCh38]
Chr17:26684529..26684530 [GRCh37]
Chr17:17q11.2
benign
NC_000017.11:g.28357342G>A single nucleotide variant not provided [RCV001572469] Chr17:28357342 [GRCh38]
Chr17:26684368 [GRCh37]
Chr17:17q11.2
likely benign
NM_152464.3(TMEM199):c.375+125G>A single nucleotide variant not provided [RCV001786623] Chr17:28359529 [GRCh38]
Chr17:26686552 [GRCh37]
Chr17:17q11.2
likely benign
NM_152464.3(TMEM199):c.19G>A (p.Ala7Thr) single nucleotide variant not provided [RCV001765717] Chr17:28357689 [GRCh38]
Chr17:26684712 [GRCh37]
Chr17:17q11.2
uncertain significance
GRCh37/hg19 17p11.2-q11.2(chr17:21690653-28281232) copy number gain not specified [RCV002052591] Chr17:21690653..28281232 [GRCh37]
Chr17:17p11.2-q11.2
pathogenic
NM_152464.3(TMEM199):c.110C>T (p.Ala37Val) single nucleotide variant not provided [RCV002041430] Chr17:28357780 [GRCh38]
Chr17:26684803 [GRCh37]
Chr17:17q11.2
uncertain significance
NM_152464.3(TMEM199):c.342A>C (p.Glu114Asp) single nucleotide variant not provided [RCV001908145] Chr17:28359371 [GRCh38]
Chr17:26686394 [GRCh37]
Chr17:17q11.2
uncertain significance
NM_152464.3(TMEM199):c.376G>C (p.Asp126His) single nucleotide variant Inborn genetic diseases [RCV002562859]|not provided [RCV001960472] Chr17:28360529 [GRCh38]
Chr17:26687552 [GRCh37]
Chr17:17q11.2
uncertain significance
NM_152464.3(TMEM199):c.74G>T (p.Arg25Leu) single nucleotide variant not provided [RCV002027276] Chr17:28357744 [GRCh38]
Chr17:26684767 [GRCh37]
Chr17:17q11.2
uncertain significance
NM_152464.3(TMEM199):c.284G>A (p.Arg95Gln) single nucleotide variant not provided [RCV002017770] Chr17:28358988 [GRCh38]
Chr17:26686011 [GRCh37]
Chr17:17q11.2
uncertain significance
NM_152464.3(TMEM199):c.376-19T>A single nucleotide variant not provided [RCV002149336] Chr17:28360510 [GRCh38]
Chr17:26687533 [GRCh37]
Chr17:17q11.2
benign
NM_152464.3(TMEM199):c.540A>G (p.Leu180=) single nucleotide variant not provided [RCV002211391] Chr17:28361165 [GRCh38]
Chr17:26688187 [GRCh37]
Chr17:17q11.2
likely benign
NM_152464.3(TMEM199):c.177C>T (p.Leu59=) single nucleotide variant not provided [RCV002131215] Chr17:28357847 [GRCh38]
Chr17:26684870 [GRCh37]
Chr17:17q11.2
likely benign
NM_152464.3(TMEM199):c.44T>C (p.Leu15Ser) single nucleotide variant not provided [RCV002135629] Chr17:28357714 [GRCh38]
Chr17:26684737 [GRCh37]
Chr17:17q11.2
benign
NC_000017.10:g.(?_26684694)_(27581367_?)dup duplication not provided [RCV003116316] Chr17:26684694..27581367 [GRCh37]
Chr17:17q11.2
uncertain significance
NC_000017.10:g.(?_26684694)_(29701173_?)dup duplication not provided [RCV003123018] Chr17:26684694..29701173 [GRCh37]
Chr17:17q11.2
uncertain significance
NM_152464.3(TMEM199):c.586G>A (p.Val196Ile) single nucleotide variant Inborn genetic diseases [RCV003282849] Chr17:28361211 [GRCh38]
Chr17:26688233 [GRCh37]
Chr17:17q11.2
uncertain significance
NM_152464.3(TMEM199):c.527C>T (p.Ala176Val) single nucleotide variant not provided [RCV002771369] Chr17:28360843 [GRCh38]
Chr17:26687866 [GRCh37]
Chr17:17q11.2
uncertain significance
NM_152464.3(TMEM199):c.335A>G (p.Asn112Ser) single nucleotide variant Inborn genetic diseases [RCV002776835] Chr17:28359364 [GRCh38]
Chr17:26686387 [GRCh37]
Chr17:17q11.2
uncertain significance
NM_152464.3(TMEM199):c.376-17C>T single nucleotide variant not provided [RCV002690108] Chr17:28360512 [GRCh38]
Chr17:26687535 [GRCh37]
Chr17:17q11.2
likely benign
NM_152464.3(TMEM199):c.569G>A (p.Gly190Asp) single nucleotide variant not provided [RCV002882268] Chr17:28361194 [GRCh38]
Chr17:26688216 [GRCh37]
Chr17:17q11.2
uncertain significance
NM_152464.3(TMEM199):c.577G>A (p.Glu193Lys) single nucleotide variant Inborn genetic diseases [RCV002733957] Chr17:28361202 [GRCh38]
Chr17:26688224 [GRCh37]
Chr17:17q11.2
uncertain significance
NM_152464.3(TMEM199):c.143C>G (p.Ser48Cys) single nucleotide variant Inborn genetic diseases [RCV002860140] Chr17:28357813 [GRCh38]
Chr17:26684836 [GRCh37]
Chr17:17q11.2
uncertain significance
NM_152464.3(TMEM199):c.428T>C (p.Leu143Ser) single nucleotide variant Inborn genetic diseases [RCV002845525] Chr17:28360744 [GRCh38]
Chr17:26687767 [GRCh37]
Chr17:17q11.2
uncertain significance
NM_152464.3(TMEM199):c.592G>T (p.Val198Leu) single nucleotide variant not provided [RCV002569915] Chr17:28361217 [GRCh38]
Chr17:26688239 [GRCh37]
Chr17:17q11.2
uncertain significance
NM_152464.3(TMEM199):c.20C>T (p.Ala7Val) single nucleotide variant not provided [RCV002912717] Chr17:28357690 [GRCh38]
Chr17:26684713 [GRCh37]
Chr17:17q11.2
uncertain significance
NM_152464.3(TMEM199):c.74G>A (p.Arg25Gln) single nucleotide variant not provided [RCV002619946] Chr17:28357744 [GRCh38]
Chr17:26684767 [GRCh37]
Chr17:17q11.2
uncertain significance
NM_152464.3(TMEM199):c.467C>T (p.Thr156Met) single nucleotide variant Inborn genetic diseases [RCV002925485] Chr17:28360783 [GRCh38]
Chr17:26687806 [GRCh37]
Chr17:17q11.2
uncertain significance
NM_152464.3(TMEM199):c.542C>G (p.Ala181Gly) single nucleotide variant Inborn genetic diseases [RCV002799205] Chr17:28361167 [GRCh38]
Chr17:26688189 [GRCh37]
Chr17:17q11.2
uncertain significance
NM_152464.3(TMEM199):c.532C>T (p.Arg178Trp) single nucleotide variant Inborn genetic diseases [RCV002923104]|not provided [RCV002941870] Chr17:28361157 [GRCh38]
Chr17:26688179 [GRCh37]
Chr17:17q11.2
uncertain significance
NM_152464.3(TMEM199):c.350G>A (p.Arg117Gln) single nucleotide variant not provided [RCV002932678] Chr17:28359379 [GRCh38]
Chr17:26686402 [GRCh37]
Chr17:17q11.2
uncertain significance
NM_152464.3(TMEM199):c.547T>C (p.Leu183=) single nucleotide variant not provided [RCV002800926] Chr17:28361172 [GRCh38]
Chr17:26688194 [GRCh37]
Chr17:17q11.2
likely benign
NM_152464.3(TMEM199):c.215C>T (p.Ser72Phe) single nucleotide variant Inborn genetic diseases [RCV002850157] Chr17:28358919 [GRCh38]
Chr17:26685942 [GRCh37]
Chr17:17q11.2
uncertain significance
NM_152464.3(TMEM199):c.16C>T (p.Leu6Phe) single nucleotide variant not provided [RCV002663198] Chr17:28357686 [GRCh38]
Chr17:26684709 [GRCh37]
Chr17:17q11.2
uncertain significance
NM_152464.3(TMEM199):c.419-11C>T single nucleotide variant not provided [RCV002597869] Chr17:28360724 [GRCh38]
Chr17:26687747 [GRCh37]
Chr17:17q11.2
benign
NM_152464.3(TMEM199):c.595C>G (p.Arg199Gly) single nucleotide variant Inborn genetic diseases [RCV002900367]|not provided [RCV002900366] Chr17:28361220 [GRCh38]
Chr17:26688242 [GRCh37]
Chr17:17q11.2
uncertain significance
NM_152464.3(TMEM199):c.455A>G (p.Asn152Ser) single nucleotide variant Inborn genetic diseases [RCV002605462]|not provided [RCV002631446] Chr17:28360771 [GRCh38]
Chr17:26687794 [GRCh37]
Chr17:17q11.2
uncertain significance
NM_152464.3(TMEM199):c.13_14del (p.Leu5fs) deletion not provided [RCV002654722] Chr17:28357682..28357683 [GRCh38]
Chr17:26684705..26684706 [GRCh37]
Chr17:17q11.2
pathogenic
NM_152464.3(TMEM199):c.419-6C>G single nucleotide variant not provided [RCV002633374] Chr17:28360729 [GRCh38]
Chr17:26687752 [GRCh37]
Chr17:17q11.2
likely benign
NM_152464.3(TMEM199):c.16C>G (p.Leu6Val) single nucleotide variant Inborn genetic diseases [RCV003181085] Chr17:28357686 [GRCh38]
Chr17:26684709 [GRCh37]
Chr17:17q11.2
uncertain significance
NM_152464.3(TMEM199):c.151C>T (p.Pro51Ser) single nucleotide variant Inborn genetic diseases [RCV003191301] Chr17:28357821 [GRCh38]
Chr17:26684844 [GRCh37]
Chr17:17q11.2
uncertain significance
NM_152464.3(TMEM199):c.268G>A (p.Val90Ile) single nucleotide variant Inborn genetic diseases [RCV003210767] Chr17:28358972 [GRCh38]
Chr17:26685995 [GRCh37]
Chr17:17q11.2
uncertain significance
GRCh37/hg19 17q11.1-11.2(chr17:25263507-27829791)x3 copy number gain Developmental delay with or without intellectual impairment or behavioral abnormalities [RCV003329553] Chr17:25263507..27829791 [GRCh37]
Chr17:17q11.1-11.2
uncertain significance
NM_152464.3(TMEM199):c.596G>A (p.Arg199Gln) single nucleotide variant not provided [RCV003726824] Chr17:28361221 [GRCh38]
Chr17:26688243 [GRCh37]
Chr17:17q11.2
uncertain significance
NM_152464.3(TMEM199):c.211+16C>T single nucleotide variant not provided [RCV003832094] Chr17:28357897 [GRCh38]
Chr17:26684920 [GRCh37]
Chr17:17q11.2
likely benign
NM_152464.3(TMEM199):c.230A>G (p.His77Arg) single nucleotide variant not provided [RCV003857454] Chr17:28358934 [GRCh38]
Chr17:26685957 [GRCh37]
Chr17:17q11.2
uncertain significance
NM_152464.3(TMEM199):c.376-10T>C single nucleotide variant not provided [RCV003554867] Chr17:28360519 [GRCh38]
Chr17:26687542 [GRCh37]
Chr17:17q11.2
likely benign
NM_152464.3(TMEM199):c.-7del deletion TMEM199-related disorder [RCV003937401] Chr17:28357663 [GRCh38]
Chr17:26684686 [GRCh37]
Chr17:17q11.2
likely benign
NM_152464.3(TMEM199):c.211+10A>G single nucleotide variant TMEM199-related disorder [RCV003899669] Chr17:28357891 [GRCh38]
Chr17:26684914 [GRCh37]
Chr17:17q11.2
likely benign
NM_152464.3(TMEM199):c.175C>T (p.Leu59Phe) single nucleotide variant Inborn genetic diseases [RCV004467442] Chr17:28357845 [GRCh38]
Chr17:26684868 [GRCh37]
Chr17:17q11.2
uncertain significance
NM_152464.3(TMEM199):c.349C>T (p.Arg117Trp) single nucleotide variant Inborn genetic diseases [RCV004467443] Chr17:28359378 [GRCh38]
Chr17:26686401 [GRCh37]
Chr17:17q11.2
uncertain significance
NM_152464.3(TMEM199):c.526G>T (p.Ala176Ser) single nucleotide variant Inborn genetic diseases [RCV004467445] Chr17:28360842 [GRCh38]
Chr17:26687865 [GRCh37]
Chr17:17q11.2
uncertain significance
NM_152464.3(TMEM199):c.530C>T (p.Ser177Leu) single nucleotide variant Inborn genetic diseases [RCV004467446] Chr17:28360846 [GRCh38]
Chr17:26687869 [GRCh37]
Chr17:17q11.2
uncertain significance
NM_152464.3(TMEM199):c.100C>T (p.Leu34Phe) single nucleotide variant Inborn genetic diseases [RCV004467441] Chr17:28357770 [GRCh38]
Chr17:26684793 [GRCh37]
Chr17:17q11.2
uncertain significance
NM_152464.3(TMEM199):c.400A>G (p.Ser134Gly) single nucleotide variant Inborn genetic diseases [RCV004686914] Chr17:28360553 [GRCh38]
Chr17:26687576 [GRCh37]
Chr17:17q11.2
uncertain significance
NM_152464.3(TMEM199):c.122A>C (p.Lys41Thr) single nucleotide variant Inborn genetic diseases [RCV004679590] Chr17:28357792 [GRCh38]
Chr17:26684815 [GRCh37]
Chr17:17q11.2
uncertain significance
NM_152464.3(TMEM199):c.385C>T (p.His129Tyr) single nucleotide variant Inborn genetic diseases [RCV004679591] Chr17:28360538 [GRCh38]
Chr17:26687561 [GRCh37]
Chr17:17q11.2
uncertain significance
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:2843
Count of miRNA genes:1094
Interacting mature miRNAs:1349
Transcripts:ENST00000292114, ENST00000395404, ENST00000483505, ENST00000509083, ENST00000555264, ENST00000577317, ENST00000580868, ENST00000581386, ENST00000585027
Prediction methods:Miranda, 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.


QTLs in Region (GRCh38)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
597303483GWAS1399557_Hlevel of probable G-protein coupled receptor 142 in blood serum QTL GWAS1399557 (human)1e-21level of probable G-protein coupled receptor 142 in blood serum172836164128361642Human
597304179GWAS1400253_Hlevel of TM2 domain-containing protein 1 in blood serum QTL GWAS1400253 (human)3e-17level of TM2 domain-containing protein 1 in blood serum172836164128361642Human
597304022GWAS1400096_Hcalcium/calmodulin-dependent protein kinase type 1D measurement QTL GWAS1400096 (human)7e-28calcium/calmodulin-dependent protein kinase type 1D measurement172836164128361642Human
597304471GWAS1400545_Hlevel of pregnancy-specific beta-1-glycoprotein 1 in blood serum QTL GWAS1400545 (human)2e-28level of pregnancy-specific beta-1-glycoprotein 1 in blood serum172836164128361642Human
597303412GWAS1399486_Hlevel of forkhead box protein O1 in blood serum QTL GWAS1399486 (human)3e-19level of forkhead box protein O1 in blood serum172836164128361642Human
597304340GWAS1400414_Hlevel of ropporin-1B in blood serum QTL GWAS1400414 (human)2e-17level of ropporin-1B in blood serum172836164128361642Human
597303755GWAS1399829_Hlevel of calsequestrin-1 in blood serum QTL GWAS1399829 (human)5e-18level of calsequestrin-1 in blood serum172836164128361642Human
597303753GWAS1399827_HBCL-2-like protein 1 measurement QTL GWAS1399827 (human)1e-12BCL-2-like protein 1 measurement172836164128361642Human
1298406BP16_HBlood pressure QTL 16 (human)0.0004Blood pressurehypertension susceptibility171477864740778647Human
597304399GWAS1400473_Hlevel of glutaredoxin-1 in blood serum QTL GWAS1400473 (human)1e-59level of glutaredoxin-1 in blood serum172836164128361642Human
597093664GWAS1189738_H3-hydroxypropylmercapturic acid measurement QTL GWAS1189738 (human)0.0000073-hydroxypropylmercapturic acid measurement172836261928362620Human
597303906GWAS1399980_Hlevel of agouti-signaling protein in blood serum QTL GWAS1399980 (human)5e-12level of agouti-signaling protein in blood serum172836164128361642Human
597274304GWAS1370378_Hvitronectin measurement QTL GWAS1370378 (human)1e-13vitronectin measurement172835942228359423Human
597235008GWAS1331082_Hblood protein measurement QTL GWAS1331082 (human)2e-27blood protein amount (VT:0005416)blood protein measurement (CMO:0000028)172836164128361642Human
597301664GWAS1397738_Hsodium- and chloride-dependent neutral and basic amino acid transporter B(0+) measurement QTL GWAS1397738 (human)2e-15sodium- and chloride-dependent neutral and basic amino acid transporter B(0+) measurement172836164128361642Human
597267301GWAS1363375_Hserine/threonine-protein kinase 16 measurement QTL GWAS1363375 (human)3e-11enzyme/coenzyme activity trait (VT:0005584)172836164128361642Human
597304678GWAS1400752_Hgrowth/differentiation factor 9 measurement QTL GWAS1400752 (human)3e-12growth/differentiation factor 9 measurement172836164128361642Human
597188868GWAS1284942_Hcholesterol in medium HDL measurement QTL GWAS1284942 (human)9e-10cholesterol in medium HDL measurement 172836164128361642Human
597122121GWAS1218195_Hblood protein measurement QTL GWAS1218195 (human)1e-31blood protein amount (VT:0005416)blood protein measurement (CMO:0000028)172836164128361642Human

Markers in Region
D17S1555  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh371726,688,873 - 26,689,051UniSTSGRCh37
Build 361723,713,000 - 23,713,178RGDNCBI36
Celera1723,550,630 - 23,550,808RGD
Cytogenetic Map17q11.2UniSTS
HuRef1722,897,281 - 22,897,459UniSTS
Cda01c02  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh371726,688,902 - 26,689,009UniSTSGRCh37
Build 361723,713,029 - 23,713,136RGDNCBI36
Celera1723,550,659 - 23,550,766RGD
Cytogenetic Map17q11.2UniSTS
HuRef1722,897,310 - 22,897,417UniSTS
SHGC-132409  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh371726,689,104 - 26,689,240UniSTSGRCh37
Build 361723,713,231 - 23,713,367RGDNCBI36
Celera1723,550,861 - 23,550,997RGD
Cytogenetic Map17q11.2UniSTS
HuRef1722,897,512 - 22,897,648UniSTS
TNG Radiation Hybrid Map1710776.0UniSTS
SHGC-30273  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh371726,689,113 - 26,689,242UniSTSGRCh37
Build 361723,713,240 - 23,713,369RGDNCBI36
Celera1723,550,870 - 23,550,999RGD
Cytogenetic Map17q11.2UniSTS
HuRef1722,897,521 - 22,897,650UniSTS


Expression

RNA-SEQ Expression

adipose tissue
alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
entire extraembryonic component
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
musculoskeletal system
nervous system
pharyngeal arch
renal system
reproductive system
respiratory system
sensory system
visual system
1204 2439 2788 2253 4974 1726 2351 6 624 1951 465 2270 7306 6472 53 3734 1 852 1744 1617 175 1

Sequence


Ensembl Acc Id: ENST00000292114   ⟹   ENSP00000292114
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1728,357,647 - 28,363,683 (+)Ensembl
Ensembl Acc Id: ENST00000395404   ⟹   ENSP00000465232
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1728,358,043 - 28,361,455 (+)Ensembl
Ensembl Acc Id: ENST00000483505
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1728,357,708 - 28,361,234 (+)Ensembl
Ensembl Acc Id: ENST00000509083
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1728,359,187 - 28,361,108 (+)Ensembl
Ensembl Acc Id: ENST00000555264   ⟹   ENSP00000462356
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1728,357,642 - 28,361,177 (+)Ensembl
Ensembl Acc Id: ENST00000579762
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1728,357,652 - 28,358,468 (+)Ensembl
Ensembl Acc Id: ENST00000580868   ⟹   ENSP00000462195
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1728,357,647 - 28,361,229 (+)Ensembl
Ensembl Acc Id: ENST00000581386
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1728,357,657 - 28,359,611 (+)Ensembl
Ensembl Acc Id: ENST00000585027
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1728,360,238 - 28,361,295 (+)Ensembl
RefSeq Acc Id: NM_152464   ⟹   NP_689677
RefSeq Status: REVIEWED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381728,357,647 - 28,363,683 (+)NCBI
GRCh371726,684,687 - 26,689,089 (+)RGD
Build 361723,708,814 - 23,713,216 (+)NCBI Archive
Celera1723,546,441 - 23,550,846 (+)RGD
HuRef1722,893,092 - 22,897,497 (+)ENTREZGENE
CHM1_11726,747,533 - 26,753,637 (+)NCBI
T2T-CHM13v2.01729,299,496 - 29,305,534 (+)NCBI
Sequence:
RefSeq Acc Id: NP_689677   ⟸   NM_152464
- UniProtKB: Q8N511 (UniProtKB/Swiss-Prot),   A8K610 (UniProtKB/TrEMBL),   Q53EQ5 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSP00000462195   ⟸   ENST00000580868
Ensembl Acc Id: ENSP00000462356   ⟸   ENST00000555264
Ensembl Acc Id: ENSP00000292114   ⟸   ENST00000292114
Ensembl Acc Id: ENSP00000465232   ⟸   ENST00000395404

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q8N511-F1-model_v2 AlphaFold Q8N511 1-208 view protein structure

Promoters
RGD ID:6794452
Promoter ID:HG_KWN:25538
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:K562
Transcripts:ENST00000003607,   ENST00000395404,   NM_015584,   OTTHUMT00000255676,   OTTHUMT00000255678,   UC002HAZ.1
Position:
Human AssemblyChrPosition (strand)Source
Build 361723,708,431 - 23,708,931 (-)MPROMDB
RGD ID:7234349
Promoter ID:EPDNEW_H22920
Type:initiation region
Name:TMEM199_1
Description:transmembrane protein 199
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Human AssemblyChrPosition (strand)Source
GRCh381728,357,647 - 28,357,707EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene HGNC:18085 AgrOrtholog
COSMIC TMEM199 COSMIC
Ensembl Genes ENSG00000244045 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Transcript ENST00000292114 ENTREZGENE
  ENST00000292114.8 UniProtKB/Swiss-Prot
  ENST00000395404.7 UniProtKB/TrEMBL
  ENST00000555264.6 UniProtKB/TrEMBL
  ENST00000580868.5 UniProtKB/TrEMBL
GTEx ENSG00000244045 GTEx
HGNC ID HGNC:18085 ENTREZGENE
Human Proteome Map TMEM199 Human Proteome Map
InterPro ATPase_Vma12 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report hsa:147007 UniProtKB/Swiss-Prot
NCBI Gene TMEM199 ENTREZGENE
OMIM 616815 OMIM
PANTHER PTHR31394 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TRANSMEMBRANE PROTEIN 199 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Vma12 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PharmGKB PA162406348 PharmGKB
UniProt A8K610 ENTREZGENE, UniProtKB/TrEMBL
  J3KRW7_HUMAN UniProtKB/TrEMBL
  J3KS81_HUMAN UniProtKB/TrEMBL
  K7EJL8_HUMAN UniProtKB/TrEMBL
  Q53EQ5 ENTREZGENE, UniProtKB/TrEMBL
  Q8N511 ENTREZGENE, UniProtKB/Swiss-Prot