Incidental Mutation 'R7899:Tcirg1'
ID 609923
Institutional Source Beutler Lab
Gene Symbol Tcirg1
Ensembl Gene ENSMUSG00000001750
Gene Name T cell, immune regulator 1, ATPase, H+ transporting, lysosomal V0 protein A3
Synonyms OC-116, TIRC7, V-ATPase a3, ATP6a3, Atp6i
MMRRC Submission 045951-MU
Accession Numbers
Essential gene? Probably essential (E-score: 0.857) question?
Stock # R7899 (G1)
Quality Score 225.009
Status Validated
Chromosome 19
Chromosomal Location 3946050-3957133 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to T at 3949104 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Isoleucine to Asparagine at position 395 (I395N)
Ref Sequence ENSEMBL: ENSMUSP00000001801 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000001801] [ENSMUST00000025760] [ENSMUST00000072055] [ENSMUST00000122885] [ENSMUST00000126070] [ENSMUST00000128694] [ENSMUST00000135070] [ENSMUST00000145791]
AlphaFold Q9JHF5
Predicted Effect probably damaging
Transcript: ENSMUST00000001801
AA Change: I395N

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000001801
Gene: ENSMUSG00000001750
AA Change: I395N

DomainStartEndE-ValueType
Pfam:V_ATPase_I 26 830 4.4e-287 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000025760
SMART Domains Protein: ENSMUSP00000025760
Gene: ENSMUSG00000024843

DomainStartEndE-ValueType
low complexity region 13 24 N/A INTRINSIC
low complexity region 53 74 N/A INTRINSIC
Pfam:APH 108 373 2.4e-11 PFAM
Pfam:Choline_kinase 135 370 8.2e-82 PFAM
Pfam:EcKinase 211 345 2.5e-7 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000072055
SMART Domains Protein: ENSMUSP00000071933
Gene: ENSMUSG00000024843

DomainStartEndE-ValueType
low complexity region 13 24 N/A INTRINSIC
low complexity region 53 74 N/A INTRINSIC
Pfam:APH 108 358 6.4e-12 PFAM
Pfam:Choline_kinase 135 352 1.6e-84 PFAM
Pfam:EcKinase 190 329 2e-7 PFAM
Predicted Effect probably damaging
Transcript: ENSMUST00000122885
AA Change: I50N

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000114768
Gene: ENSMUSG00000001750
AA Change: I50N

DomainStartEndE-ValueType
Pfam:V_ATPase_I 1 91 2.9e-44 PFAM
Predicted Effect probably damaging
Transcript: ENSMUST00000126070
AA Change: I395N

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000120531
Gene: ENSMUSG00000001750
AA Change: I395N

DomainStartEndE-ValueType
Pfam:V_ATPase_I 27 829 1.2e-277 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000128694
SMART Domains Protein: ENSMUSP00000119919
Gene: ENSMUSG00000024843

DomainStartEndE-ValueType
PDB:4DA5|B 1 150 2e-60 PDB
Predicted Effect probably benign
Transcript: ENSMUST00000132164
AA Change: S183T

PolyPhen 2 Score 0.016 (Sensitivity: 0.95; Specificity: 0.79)
SMART Domains Protein: ENSMUSP00000120968
Gene: ENSMUSG00000001750
AA Change: S183T

DomainStartEndE-ValueType
Pfam:V_ATPase_I 1 190 4.5e-48 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000135070
SMART Domains Protein: ENSMUSP00000121241
Gene: ENSMUSG00000001750

DomainStartEndE-ValueType
low complexity region 59 70 N/A INTRINSIC
Predicted Effect probably damaging
Transcript: ENSMUST00000145791
AA Change: I395N

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000122474
Gene: ENSMUSG00000001750
AA Change: I395N

DomainStartEndE-ValueType
Pfam:V_ATPase_I 26 830 4.4e-287 PFAM
Meta Mutation Damage Score 0.9363 question?
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 99.9%
  • 10x: 99.6%
  • 20x: 98.8%
Validation Efficiency 97% (70/72)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] Through alternate splicing, this gene encodes two proteins with similarity to subunits of the vacuolar ATPase (V-ATPase) but the encoded proteins seem to have different functions. V-ATPase is a multisubunit enzyme that mediates acidification of eukaryotic intracellular organelles. V-ATPase dependent organelle acidification is necessary for such intracellular processes as protein sorting, zymogen activation, and receptor-mediated endocytosis. V-ATPase is comprised of a cytosolic V1 domain and a transmembrane V0 domain. Mutations in this gene are associated with infantile malignant osteopetrosis. [provided by RefSeq, Jul 2008]
PHENOTYPE: Homozygotes for mutant alleles exhibit severe osteopetrosis with increased bone density due to failure of secondary bone resorption. Mutants lack teeth and die around 30-40 days of age. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 75 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
1500011B03Rik T C 5: 114,947,381 (GRCm39) T49A possibly damaging Het
A530084C06Rik G T 13: 31,742,978 (GRCm39) R92S unknown Het
Aagab T C 9: 63,524,132 (GRCm39) F80L probably benign Het
Aox1 A G 1: 58,320,396 (GRCm39) probably null Het
Arhgef2 T C 3: 88,528,569 (GRCm39) S2P probably damaging Het
Bcar3 T G 3: 122,301,902 (GRCm39) V199G probably damaging Het
C1ra G A 6: 124,494,684 (GRCm39) E316K probably benign Het
Cacna1a G A 8: 85,320,802 (GRCm39) V1587M possibly damaging Het
Caps2 C A 10: 112,001,666 (GRCm39) S19Y possibly damaging Het
Ccdc196 A G 12: 78,244,196 (GRCm39) N50D Het
Cep89 G A 7: 35,129,353 (GRCm39) R630H probably damaging Het
Cobll1 A G 2: 64,956,275 (GRCm39) C328R probably damaging Het
Colec11 A C 12: 28,645,281 (GRCm39) V130G probably damaging Het
Dennd5b A T 6: 148,943,159 (GRCm39) D572E probably damaging Het
Dido1 A T 2: 180,313,390 (GRCm39) S961T possibly damaging Het
Dnah7c A T 1: 46,553,861 (GRCm39) M380L probably benign Het
Dnai2 T C 11: 114,629,456 (GRCm39) I161T probably benign Het
Dnttip2 T A 3: 122,076,018 (GRCm39) M650K probably damaging Het
Dpp6 C T 5: 27,926,077 (GRCm39) P717L probably benign Het
Epha10 A G 4: 124,808,628 (GRCm39) E759G Het
Frmd4a T C 2: 4,608,900 (GRCm39) W923R probably damaging Het
Ftsj3 C A 11: 106,143,115 (GRCm39) E400* probably null Het
Gabra4 C A 5: 71,815,338 (GRCm39) probably benign Het
Gfm1 T A 3: 67,380,860 (GRCm39) N658K probably benign Het
Gm21560 A T 14: 6,218,220 (GRCm38) I86N probably damaging Het
Gpr68 C A 12: 100,844,707 (GRCm39) C279F probably damaging Het
Hspg2 G A 4: 137,275,427 (GRCm39) A2752T possibly damaging Het
Hydin A T 8: 111,314,380 (GRCm39) D4288V probably benign Het
Ift74 A G 4: 94,510,214 (GRCm39) T82A possibly damaging Het
Ints7 T A 1: 191,353,427 (GRCm39) W918R probably damaging Het
Kcnc1 T A 7: 46,077,245 (GRCm39) I349N probably damaging Het
Loxl1 C T 9: 58,198,117 (GRCm39) D580N probably damaging Het
Mlph A T 1: 90,869,485 (GRCm39) R496* probably null Het
Mtdh A G 15: 34,123,865 (GRCm39) D364G possibly damaging Het
Mtmr11 C A 3: 96,077,744 (GRCm39) L580I probably damaging Het
Muc16 T C 9: 18,551,993 (GRCm39) I4767V probably benign Het
Muc21 TCAGGGTGGGGGTAGAGCCTGAGCCACTGCTAGATGCAGTGGTGGGCAGGGTGGGGGTAGAGCCTGAG TCAGGGTGGGGGTAGAGCCTGAG 17: 35,931,493 (GRCm39) probably benign Het
Myot A G 18: 44,487,251 (GRCm39) T363A probably benign Het
Nfxl1 G A 5: 72,681,558 (GRCm39) P658S probably damaging Het
Nhlrc3 A C 3: 53,369,080 (GRCm39) S120A probably benign Het
Nmur2 C A 11: 55,931,161 (GRCm39) Q183H probably benign Het
Nucb2 T A 7: 116,121,205 (GRCm39) I45K probably benign Het
Nup155 A T 15: 8,148,663 (GRCm39) D277V probably damaging Het
Or5ak25 T C 2: 85,268,741 (GRCm39) T254A probably benign Het
Orc1 T G 4: 108,460,568 (GRCm39) probably null Het
Panx2 A G 15: 88,952,936 (GRCm39) T468A possibly damaging Het
Pcdh7 A G 5: 57,877,152 (GRCm39) S236G probably benign Het
Pcdhga2 G C 18: 37,803,910 (GRCm39) G585R probably damaging Het
Perm1 TGCCTCTGAGCCTGACACGGCTTTGTCTACACCCGCCTCTGAGCCTGACACGGCTTTGTCTACACCCGCCTCTGAGCCTGACACGGCTTTGTCTACACCCGCCTCT TGCCTCTGAGCCTGACACGGCTTTGTCTACACCCGCCTCTGAGCCTGACACGGCTTTGTCTACACCCGCCTCT 4: 156,302,525 (GRCm39) probably benign Het
Pgr T G 9: 8,903,743 (GRCm39) M588R probably benign Het
Ptpn18 A T 1: 34,508,986 (GRCm39) probably null Het
Rbm8a2 T A 1: 175,806,207 (GRCm39) H90L probably benign Het
Ryr3 A T 2: 112,477,295 (GRCm39) L4507Q possibly damaging Het
Serpina12 A G 12: 104,004,524 (GRCm39) V36A probably benign Het
Sis T A 3: 72,844,584 (GRCm39) S717C probably damaging Het
Slit2 A G 5: 48,404,527 (GRCm39) E846G possibly damaging Het
Smr3a C T 5: 88,156,086 (GRCm39) H85Y unknown Het
Sned1 G C 1: 93,201,804 (GRCm39) R590P probably benign Het
Spata31h1 A G 10: 82,118,731 (GRCm39) S4760P unknown Het
Sting1 A G 18: 35,867,626 (GRCm39) S357P probably damaging Het
Sult2a7 A G 7: 14,199,134 (GRCm39) Y298H probably damaging Het
Syn3 A G 10: 85,900,793 (GRCm39) V365A possibly damaging Het
Syne1 A T 10: 5,177,956 (GRCm39) Y4839* probably null Het
Taf4 G A 2: 179,573,822 (GRCm39) T682M probably damaging Het
Tbl3 G T 17: 24,921,458 (GRCm39) H478N probably damaging Het
Ticrr T C 7: 79,319,233 (GRCm39) I406T probably benign Het
Tmem120a C A 5: 135,766,052 (GRCm39) K123N probably benign Het
Tmem184c A G 8: 78,324,440 (GRCm39) V350A probably damaging Het
Tmem70 G T 1: 16,747,268 (GRCm39) M128I probably benign Het
Tmx3 A T 18: 90,545,998 (GRCm39) probably null Het
Topors G C 4: 40,260,356 (GRCm39) S976W unknown Het
Trp53 T C 11: 69,481,519 (GRCm39) L341P probably damaging Het
Usp14 T C 18: 10,000,563 (GRCm39) K366E possibly damaging Het
Zbtb49 G T 5: 38,371,274 (GRCm39) C202* probably null Het
Zkscan5 A C 5: 145,157,676 (GRCm39) H726P probably damaging Het
Other mutations in Tcirg1
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00488:Tcirg1 APN 19 3,949,108 (GRCm39) missense possibly damaging 0.94
IGL01735:Tcirg1 APN 19 3,954,210 (GRCm39) splice site probably benign
IGL03143:Tcirg1 APN 19 3,948,811 (GRCm39) missense probably damaging 1.00
R0732:Tcirg1 UTSW 19 3,947,866 (GRCm39) missense possibly damaging 0.56
R1131:Tcirg1 UTSW 19 3,946,301 (GRCm39) missense probably damaging 1.00
R1223:Tcirg1 UTSW 19 3,948,733 (GRCm39) missense probably benign 0.01
R1548:Tcirg1 UTSW 19 3,946,845 (GRCm39) missense probably benign 0.03
R1867:Tcirg1 UTSW 19 3,948,835 (GRCm39) missense probably damaging 1.00
R1926:Tcirg1 UTSW 19 3,952,843 (GRCm39) intron probably benign
R2262:Tcirg1 UTSW 19 3,953,591 (GRCm39) missense possibly damaging 0.89
R4367:Tcirg1 UTSW 19 3,949,069 (GRCm39) missense probably damaging 1.00
R5327:Tcirg1 UTSW 19 3,952,342 (GRCm39) critical splice donor site probably null
R5417:Tcirg1 UTSW 19 3,953,509 (GRCm39) splice site probably null
R5551:Tcirg1 UTSW 19 3,948,858 (GRCm39) missense probably damaging 1.00
R5930:Tcirg1 UTSW 19 3,952,424 (GRCm39) missense possibly damaging 0.95
R6026:Tcirg1 UTSW 19 3,947,487 (GRCm39) missense probably benign
R6517:Tcirg1 UTSW 19 3,951,933 (GRCm39) missense probably damaging 1.00
R7039:Tcirg1 UTSW 19 3,946,666 (GRCm39) missense probably damaging 1.00
R7181:Tcirg1 UTSW 19 3,953,576 (GRCm39) missense probably null 0.56
R7422:Tcirg1 UTSW 19 3,949,008 (GRCm39) missense possibly damaging 0.61
R7631:Tcirg1 UTSW 19 3,947,160 (GRCm39) missense probably damaging 1.00
R7768:Tcirg1 UTSW 19 3,952,900 (GRCm39) missense possibly damaging 0.91
R8110:Tcirg1 UTSW 19 3,949,099 (GRCm39) missense probably damaging 1.00
R8535:Tcirg1 UTSW 19 3,946,324 (GRCm39) missense probably damaging 1.00
R9233:Tcirg1 UTSW 19 3,952,543 (GRCm39) missense probably damaging 1.00
R9292:Tcirg1 UTSW 19 3,947,840 (GRCm39) missense probably damaging 1.00
R9611:Tcirg1 UTSW 19 3,953,400 (GRCm39) missense probably benign 0.09
R9695:Tcirg1 UTSW 19 3,952,360 (GRCm39) missense probably null 0.69
Z1176:Tcirg1 UTSW 19 3,953,425 (GRCm39) missense probably benign 0.00
Predicted Primers PCR Primer
(F):5'- AGGCTGTTCCACTCTTGTGC -3'
(R):5'- TAAACCTATGTCCACAGCCTGG -3'

Sequencing Primer
(F):5'- GTTCCACTCTTGTGCCCTATC -3'
(R):5'- GGCACTGAGATCTCCATTTTACAAG -3'
Posted On 2019-12-20