Incidental Mutation 'R4763:Atp2c1'
ID 357039
Institutional Source Beutler Lab
Gene Symbol Atp2c1
Ensembl Gene ENSMUSG00000032570
Gene Name ATPase, Ca++-sequestering
Synonyms ATP2C1A, D930003G21Rik, SPCA, 1700121J11Rik, PMR1
MMRRC Submission 042404-MU
Accession Numbers
Essential gene? Possibly non essential (E-score: 0.371) question?
Stock # R4763 (G1)
Quality Score 225
Status Validated
Chromosome 9
Chromosomal Location 105288561-105398456 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 105295766 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Threonine to Alanine at position 653 (T653A)
Ref Sequence ENSEMBL: ENSMUSP00000135802 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000038118] [ENSMUST00000085133] [ENSMUST00000112558] [ENSMUST00000163879] [ENSMUST00000177293] [ENSMUST00000176770] [ENSMUST00000177074]
AlphaFold Q80XR2
Predicted Effect probably damaging
Transcript: ENSMUST00000038118
AA Change: T789A

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000039103
Gene: ENSMUSG00000032570
AA Change: T789A

DomainStartEndE-ValueType
Cation_ATPase_N 25 99 1.85e-14 SMART
Pfam:E1-E2_ATPase 105 339 2.3e-75 PFAM
Pfam:Hydrolase 343 655 2.9e-31 PFAM
Pfam:HAD 346 652 7.7e-15 PFAM
Pfam:Hydrolase_like2 408 492 9.5e-20 PFAM
low complexity region 706 721 N/A INTRINSIC
Pfam:Cation_ATPase_C 725 897 4e-47 PFAM
Predicted Effect probably damaging
Transcript: ENSMUST00000085133
AA Change: T823A

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000082220
Gene: ENSMUSG00000032570
AA Change: T823A

DomainStartEndE-ValueType
Cation_ATPase_N 59 133 1.85e-14 SMART
Pfam:E1-E2_ATPase 138 372 3.4e-62 PFAM
Pfam:Hydrolase 377 689 2.6e-23 PFAM
Pfam:HAD 380 686 7.8e-14 PFAM
Pfam:Cation_ATPase 442 526 3.2e-19 PFAM
low complexity region 740 755 N/A INTRINSIC
Pfam:Cation_ATPase_C 759 931 3.8e-48 PFAM
Predicted Effect noncoding transcript
Transcript: ENSMUST00000112557
Predicted Effect probably damaging
Transcript: ENSMUST00000112558
AA Change: T789A

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000108177
Gene: ENSMUSG00000032570
AA Change: T789A

DomainStartEndE-ValueType
Cation_ATPase_N 25 99 1.85e-14 SMART
Pfam:E1-E2_ATPase 105 339 2.3e-75 PFAM
Pfam:Hydrolase 343 655 2.9e-31 PFAM
Pfam:HAD 346 652 7.7e-15 PFAM
Pfam:Hydrolase_like2 408 492 9.5e-20 PFAM
low complexity region 706 721 N/A INTRINSIC
Pfam:Cation_ATPase_C 725 897 4e-47 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000163879
SMART Domains Protein: ENSMUSP00000129617
Gene: ENSMUSG00000032570

DomainStartEndE-ValueType
Cation_ATPase_N 9 83 1.85e-14 SMART
Pfam:E1-E2_ATPase 89 323 5.2e-76 PFAM
Pfam:Hydrolase 327 639 5.6e-32 PFAM
Pfam:HAD 330 636 1.4e-15 PFAM
Pfam:Hydrolase_like2 392 476 3.2e-20 PFAM
Predicted Effect noncoding transcript
Transcript: ENSMUST00000175697
Predicted Effect noncoding transcript
Transcript: ENSMUST00000176656
Predicted Effect probably damaging
Transcript: ENSMUST00000177293
AA Change: T653A

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000135802
Gene: ENSMUSG00000032570
AA Change: T653A

DomainStartEndE-ValueType
Pfam:E1-E2_ATPase 1 203 6.7e-64 PFAM
Pfam:Hydrolase 207 519 7.4e-32 PFAM
Pfam:HAD 210 516 1.9e-15 PFAM
Pfam:Hydrolase_like2 272 356 3.8e-20 PFAM
transmembrane domain 564 586 N/A INTRINSIC
Pfam:Cation_ATPase_C 589 761 1.2e-47 PFAM
Predicted Effect probably damaging
Transcript: ENSMUST00000176770
AA Change: T784A

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000134764
Gene: ENSMUSG00000032570
AA Change: T784A

DomainStartEndE-ValueType
Pfam:E1-E2_ATPase 100 334 8.9e-76 PFAM
Pfam:Hydrolase 338 650 1.1e-31 PFAM
Pfam:HAD 341 647 2.7e-15 PFAM
Pfam:Hydrolase_like2 403 487 4.8e-20 PFAM
low complexity region 701 716 N/A INTRINSIC
Pfam:Cation_ATPase_C 720 892 1.6e-47 PFAM
Predicted Effect probably damaging
Transcript: ENSMUST00000177074
AA Change: T789A

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000135646
Gene: ENSMUSG00000032570
AA Change: T789A

DomainStartEndE-ValueType
Cation_ATPase_N 25 99 1.85e-14 SMART
Pfam:E1-E2_ATPase 105 339 8.2e-76 PFAM
Pfam:Hydrolase 343 655 1e-31 PFAM
Pfam:HAD 346 652 2.5e-15 PFAM
Pfam:Hydrolase_like2 408 492 4.5e-20 PFAM
low complexity region 706 721 N/A INTRINSIC
Pfam:Cation_ATPase_C 725 886 7e-44 PFAM
Meta Mutation Damage Score 0.6309 question?
Coding Region Coverage
  • 1x: 99.1%
  • 3x: 98.5%
  • 10x: 96.9%
  • 20x: 94.3%
Validation Efficiency 97% (73/75)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The protein encoded by this gene belongs to the family of P-type cation transport ATPases. This magnesium-dependent enzyme catalyzes the hydrolysis of ATP coupled with the transport of calcium ions. Defects in this gene cause Hailey-Hailey disease, an autosomal dominant disorder. Alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Aug 2011]
PHENOTYPE: Mice homozygous for a knock-out allele show embryonic growth retardation, failure of rostral neural tube closure, Golgi and endoplasmic reticulum stress, increased apoptosis, accumulation of intracellular lipid droplets and midgestational lethality. Agedheterozygotes develop squamous cell tumors. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 64 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
2610303G11Rik A G 9: 98,069,176 (GRCm39) noncoding transcript Het
Abhd2 A G 7: 79,009,879 (GRCm39) E418G probably benign Het
Acox2 G T 14: 8,241,334 (GRCm38) H593N possibly damaging Het
Adam17 A G 12: 21,384,016 (GRCm39) Y495H probably benign Het
Afg3l2 G T 18: 67,554,329 (GRCm39) L458M probably damaging Het
Arhgap44 A G 11: 64,929,991 (GRCm39) I240T probably damaging Het
Atxn7l1 G A 12: 33,408,877 (GRCm39) probably benign Het
Cacng8 T C 7: 3,463,508 (GRCm39) V220A probably damaging Het
Card14 A T 11: 119,234,001 (GRCm39) S864C probably damaging Het
Cfap58 C T 19: 47,971,945 (GRCm39) A625V probably damaging Het
Cfap61 T C 2: 145,859,287 (GRCm39) V425A probably benign Het
Cfap73 A G 5: 120,768,294 (GRCm39) F155L probably damaging Het
Cntrl G T 2: 35,065,563 (GRCm39) R2235L probably damaging Het
Cxxc1 A G 18: 74,352,484 (GRCm39) K355E probably damaging Het
Disc1 G A 8: 125,851,277 (GRCm39) G387D probably damaging Het
Dpf2 T C 19: 5,952,480 (GRCm39) Y286C probably damaging Het
E2f7 A T 10: 110,616,710 (GRCm39) K650M probably damaging Het
Fbln2 C T 6: 91,246,982 (GRCm39) S1027F probably damaging Het
Foxj2 G T 6: 122,810,230 (GRCm39) Q196H probably benign Het
Gm6811 A G 17: 21,314,109 (GRCm39) noncoding transcript Het
Gtf2i T C 5: 134,284,818 (GRCm39) K409E probably damaging Het
Hamp T A 7: 30,641,989 (GRCm39) R55S probably damaging Het
Heatr1 C T 13: 12,445,811 (GRCm39) T1596I possibly damaging Het
Hells T C 19: 38,945,643 (GRCm39) V601A probably damaging Het
Ighv5-8 A G 12: 113,617,161 (GRCm39) S34P probably damaging Het
Lig4 T C 8: 10,022,955 (GRCm39) D275G probably damaging Het
Meak7 A G 8: 120,495,122 (GRCm39) V212A probably benign Het
Med6 T C 12: 81,629,435 (GRCm39) D59G probably damaging Het
Men1 T C 19: 6,385,102 (GRCm39) probably null Het
Mlec G A 5: 115,295,972 (GRCm39) A41V unknown Het
Ncoa1 G A 12: 4,325,297 (GRCm39) T927I probably damaging Het
Neb T A 2: 52,216,732 (GRCm39) K148* probably null Het
Neb T A 2: 52,127,052 (GRCm39) K378* probably null Het
Or4b13 T A 2: 90,082,807 (GRCm39) Y175F probably damaging Het
Or4k41 T A 2: 111,280,023 (GRCm39) C179* probably null Het
Or5p73 G A 7: 108,065,393 (GRCm39) M287I probably benign Het
Or8g26 A G 9: 39,096,256 (GRCm39) T261A probably benign Het
Parp10 C T 15: 76,117,627 (GRCm39) V920M probably damaging Het
Parp6 C A 9: 59,538,648 (GRCm39) P241H probably damaging Het
Pcyox1l A G 18: 61,830,850 (GRCm39) Y341H probably benign Het
Pfas A T 11: 68,881,020 (GRCm39) D1080E possibly damaging Het
Pi4kb G T 3: 94,911,720 (GRCm39) probably benign Het
Piwil2 C T 14: 70,614,227 (GRCm39) V846M probably damaging Het
Pkd1l2 A G 8: 117,746,168 (GRCm39) F1941L probably damaging Het
Pot1b G A 17: 56,002,160 (GRCm39) T138M possibly damaging Het
Ppp4r1 T C 17: 66,142,105 (GRCm39) I720T possibly damaging Het
Prr12 A G 7: 44,697,119 (GRCm39) L932S unknown Het
Rnaseh2a T A 8: 85,692,021 (GRCm39) E84V probably benign Het
Rpl18a G A 8: 71,348,330 (GRCm39) R118C probably benign Het
Rprm C A 2: 53,975,228 (GRCm39) C30F possibly damaging Het
Sbf2 G T 7: 110,020,124 (GRCm39) L579I probably damaging Het
Sfn C A 4: 133,328,656 (GRCm39) R142L probably benign Het
St8sia6 T C 2: 13,677,341 (GRCm39) K159E probably damaging Het
Sugct A T 13: 17,837,372 (GRCm39) F86L probably damaging Het
Tmcc3 T C 10: 94,415,173 (GRCm39) S292P probably damaging Het
Tmem33 A T 5: 67,443,479 (GRCm39) I219F probably benign Het
Trav8-1 C A 14: 53,707,492 (GRCm39) T44K possibly damaging Het
U2surp A G 9: 95,393,844 (GRCm39) probably benign Het
Use1 T C 8: 71,819,952 (GRCm39) L25P probably damaging Het
Vmn1r221 G T 13: 23,401,958 (GRCm39) noncoding transcript Het
Vmn1r50 C T 6: 90,085,062 (GRCm39) T269I probably benign Het
Washc3 A G 10: 88,055,185 (GRCm39) D125G probably damaging Het
Zfp142 G A 1: 74,615,671 (GRCm39) H278Y probably damaging Het
Zfp418 A G 7: 7,184,444 (GRCm39) N136D possibly damaging Het
Other mutations in Atp2c1
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00984:Atp2c1 APN 9 105,295,778 (GRCm39) missense probably damaging 1.00
IGL01682:Atp2c1 APN 9 105,330,041 (GRCm39) missense probably damaging 1.00
IGL01874:Atp2c1 APN 9 105,326,024 (GRCm39) missense probably damaging 1.00
IGL02299:Atp2c1 APN 9 105,338,286 (GRCm39) unclassified probably benign
IGL03186:Atp2c1 APN 9 105,290,329 (GRCm39) missense probably benign 0.10
IGL03212:Atp2c1 APN 9 105,322,466 (GRCm39) missense probably damaging 1.00
BB002:Atp2c1 UTSW 9 105,319,969 (GRCm39) missense possibly damaging 0.92
BB012:Atp2c1 UTSW 9 105,319,969 (GRCm39) missense possibly damaging 0.92
IGL02799:Atp2c1 UTSW 9 105,290,242 (GRCm39) unclassified probably benign
IGL03047:Atp2c1 UTSW 9 105,398,206 (GRCm39) intron probably benign
R0885:Atp2c1 UTSW 9 105,298,772 (GRCm39) critical splice donor site probably null
R1072:Atp2c1 UTSW 9 105,336,943 (GRCm39) missense possibly damaging 0.92
R1469:Atp2c1 UTSW 9 105,312,351 (GRCm39) nonsense probably null
R1469:Atp2c1 UTSW 9 105,312,351 (GRCm39) nonsense probably null
R1611:Atp2c1 UTSW 9 105,320,051 (GRCm39) missense probably damaging 0.98
R1638:Atp2c1 UTSW 9 105,309,897 (GRCm39) missense probably damaging 0.96
R1667:Atp2c1 UTSW 9 105,309,996 (GRCm39) missense probably null 0.94
R1722:Atp2c1 UTSW 9 105,316,599 (GRCm39) missense probably benign 0.01
R1734:Atp2c1 UTSW 9 105,291,854 (GRCm39) missense probably damaging 1.00
R1782:Atp2c1 UTSW 9 105,308,786 (GRCm39) missense probably damaging 0.99
R1964:Atp2c1 UTSW 9 105,323,322 (GRCm39) missense probably damaging 1.00
R2008:Atp2c1 UTSW 9 105,309,925 (GRCm39) missense probably benign 0.00
R2093:Atp2c1 UTSW 9 105,295,320 (GRCm39) nonsense probably null
R3720:Atp2c1 UTSW 9 105,300,175 (GRCm39) missense probably damaging 1.00
R4118:Atp2c1 UTSW 9 105,343,858 (GRCm39) missense probably damaging 1.00
R4273:Atp2c1 UTSW 9 105,312,339 (GRCm39) missense probably benign 0.10
R4962:Atp2c1 UTSW 9 105,320,149 (GRCm39) missense probably benign 0.03
R5121:Atp2c1 UTSW 9 105,326,024 (GRCm39) missense probably damaging 1.00
R5458:Atp2c1 UTSW 9 105,291,924 (GRCm39) nonsense probably null
R5551:Atp2c1 UTSW 9 105,336,936 (GRCm39) missense probably damaging 1.00
R6198:Atp2c1 UTSW 9 105,398,271 (GRCm39) missense probably benign 0.00
R6414:Atp2c1 UTSW 9 105,343,855 (GRCm39) missense probably damaging 1.00
R6432:Atp2c1 UTSW 9 105,322,512 (GRCm39) missense probably damaging 1.00
R6675:Atp2c1 UTSW 9 105,330,732 (GRCm39) critical splice donor site probably null
R6719:Atp2c1 UTSW 9 105,301,377 (GRCm39) missense probably damaging 1.00
R6777:Atp2c1 UTSW 9 105,295,799 (GRCm39) missense possibly damaging 0.64
R6847:Atp2c1 UTSW 9 105,295,778 (GRCm39) missense probably damaging 1.00
R6870:Atp2c1 UTSW 9 105,347,261 (GRCm39) missense probably benign 0.13
R7097:Atp2c1 UTSW 9 105,341,850 (GRCm39) missense probably damaging 1.00
R7120:Atp2c1 UTSW 9 105,297,385 (GRCm39) nonsense probably null
R7216:Atp2c1 UTSW 9 105,344,930 (GRCm39) missense probably benign 0.00
R7284:Atp2c1 UTSW 9 105,398,008 (GRCm39) splice site probably null
R7365:Atp2c1 UTSW 9 105,300,198 (GRCm39) missense probably damaging 1.00
R7448:Atp2c1 UTSW 9 105,329,982 (GRCm39) missense probably damaging 0.98
R7818:Atp2c1 UTSW 9 105,291,956 (GRCm39) missense probably benign 0.06
R7921:Atp2c1 UTSW 9 105,291,886 (GRCm39) missense probably damaging 1.00
R7925:Atp2c1 UTSW 9 105,319,969 (GRCm39) missense possibly damaging 0.92
R8088:Atp2c1 UTSW 9 105,329,768 (GRCm39) splice site probably null
R8257:Atp2c1 UTSW 9 105,308,756 (GRCm39) missense probably benign 0.40
R8260:Atp2c1 UTSW 9 105,295,778 (GRCm39) missense probably damaging 1.00
R8265:Atp2c1 UTSW 9 105,347,315 (GRCm39) missense probably benign 0.01
R8307:Atp2c1 UTSW 9 105,320,030 (GRCm39) missense probably benign
R9052:Atp2c1 UTSW 9 105,330,032 (GRCm39) missense probably damaging 0.99
R9066:Atp2c1 UTSW 9 105,330,845 (GRCm39) missense probably damaging 1.00
R9177:Atp2c1 UTSW 9 105,336,858 (GRCm39) critical splice donor site probably null
R9257:Atp2c1 UTSW 9 105,291,851 (GRCm39) nonsense probably null
R9566:Atp2c1 UTSW 9 105,343,828 (GRCm39) missense probably damaging 0.97
R9779:Atp2c1 UTSW 9 105,291,919 (GRCm39) missense probably damaging 0.98
X0053:Atp2c1 UTSW 9 105,295,883 (GRCm39) missense probably damaging 1.00
Predicted Primers PCR Primer
(F):5'- CAAACTTGCATGTACACGGTAC -3'
(R):5'- TCCCTAGCTAATAGATGCTAGTTAGG -3'

Sequencing Primer
(F):5'- CATGTACACGGTACTTTACTAAAGGC -3'
(R):5'- TAAGCCTTGGAGTAGAGC -3'
Posted On 2015-11-11