Incidental Mutation 'R6346:Vps13a'
ID 513979
Institutional Source Beutler Lab
Gene Symbol Vps13a
Ensembl Gene ENSMUSG00000046230
Gene Name vacuolar protein sorting 13A
Synonyms 4930543C13Rik, D330038K10Rik, 4930516E05Rik
MMRRC Submission 044500-MU
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R6346 (G1)
Quality Score 225.009
Status Validated
Chromosome 19
Chromosomal Location 16592730-16758297 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 16659578 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Isoleucine to Valine at position 1650 (I1650V)
Ref Sequence ENSEMBL: ENSMUSP00000153129 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000068156] [ENSMUST00000224149]
AlphaFold no structure available at present
Predicted Effect possibly damaging
Transcript: ENSMUST00000068156
AA Change: I1650V

PolyPhen 2 Score 0.482 (Sensitivity: 0.89; Specificity: 0.90)
SMART Domains Protein: ENSMUSP00000068716
Gene: ENSMUSG00000046230
AA Change: I1650V

DomainStartEndE-ValueType
Pfam:Chorein_N 3 117 5.4e-38 PFAM
Pfam:VPS13 139 371 3.7e-64 PFAM
low complexity region 553 563 N/A INTRINSIC
Pfam:VPS13_mid_rpt 567 791 1.4e-69 PFAM
Pfam:VPS13_mid_rpt 1138 1329 2e-10 PFAM
low complexity region 1367 1377 N/A INTRINSIC
Blast:INB 1575 1855 1e-149 BLAST
Pfam:SHR-BD 2200 2449 1.3e-35 PFAM
low complexity region 2510 2521 N/A INTRINSIC
low complexity region 2632 2648 N/A INTRINSIC
low complexity region 2719 2731 N/A INTRINSIC
Pfam:VPS13_C 2755 2935 8.9e-66 PFAM
Pfam:ATG_C 2938 3029 1.6e-16 PFAM
Predicted Effect noncoding transcript
Transcript: ENSMUST00000223897
Predicted Effect possibly damaging
Transcript: ENSMUST00000224149
AA Change: I1650V

PolyPhen 2 Score 0.937 (Sensitivity: 0.80; Specificity: 0.94)
Predicted Effect noncoding transcript
Transcript: ENSMUST00000225349
Meta Mutation Damage Score 0.2785 question?
Coding Region Coverage
  • 1x: 99.9%
  • 3x: 99.6%
  • 10x: 98.1%
  • 20x: 94.6%
Validation Efficiency 98% (41/42)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The protein encoded by this gene may control steps in the cycling of proteins through the trans-Golgi network to endosomes, lysosomes and the plasma membrane. Mutations in this gene cause the autosomal recessive disorder, chorea-acanthocytosis. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Jul 2008]
PHENOTYPE: Aging mice homozygous for a knock-out allele display motor dysfunction and abnormal social interaction, hematologic anomalies including acanthocytosis, selective atrophy of the striatum with significant apoptosis and gliosis, and reduced homovanillic acid levels in midbrain. [provided by MGI curators]
Allele List at MGI

All alleles(8) : Targeted(3) Gene trapped(5)

Other mutations in this stock
Total: 43 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Akap13 C T 7: 75,335,002 (GRCm39) S455L probably damaging Het
Apbb1ip T G 2: 22,757,005 (GRCm39) probably null Het
Arhgap18 A T 10: 26,722,061 (GRCm39) I11F probably damaging Het
Arl14epl A T 18: 47,059,409 (GRCm39) N8I possibly damaging Het
Atp4a T A 7: 30,414,781 (GRCm39) I190N possibly damaging Het
Bfar T C 16: 13,519,997 (GRCm39) F285S probably damaging Het
Carf C T 1: 60,180,699 (GRCm39) Q409* probably null Het
Cd244a T C 1: 171,404,889 (GRCm39) V247A probably damaging Het
Ceacam12 T A 7: 17,803,326 (GRCm39) I244K probably damaging Het
Cmya5 T C 13: 93,228,698 (GRCm39) E2130G probably damaging Het
Cyp2b23 T G 7: 26,381,150 (GRCm39) H69P probably damaging Het
Dixdc1 T C 9: 50,595,253 (GRCm39) Q183R probably damaging Het
Dock10 T A 1: 80,553,573 (GRCm39) probably null Het
Fam20c T C 5: 138,752,450 (GRCm39) F279S probably damaging Het
Hcn4 C T 9: 58,766,327 (GRCm39) T665I unknown Het
Helz2 C T 2: 180,875,260 (GRCm39) E1745K probably damaging Het
Kdm7a A T 6: 39,128,145 (GRCm39) probably null Het
Ksr1 A C 11: 78,910,490 (GRCm39) L814R possibly damaging Het
Lmnb1 A G 18: 56,876,310 (GRCm39) I473V probably benign Het
Mllt3 T C 4: 87,759,445 (GRCm39) K201R probably damaging Het
Myo1b C T 1: 51,823,666 (GRCm39) C413Y probably damaging Het
Myom3 A T 4: 135,533,362 (GRCm39) N1185I probably benign Het
Nrde2 A G 12: 100,098,565 (GRCm39) S701P probably benign Het
Ntn4 A T 10: 93,480,723 (GRCm39) D112V probably damaging Het
Nup43 T A 10: 7,550,826 (GRCm39) V232D probably damaging Het
Pcdha6 G A 18: 37,101,113 (GRCm39) C102Y probably damaging Het
Pcdhgb8 T C 18: 37,895,131 (GRCm39) L67P probably damaging Het
Pkd1l3 A G 8: 110,358,016 (GRCm39) H836R probably damaging Het
Plekha1 T A 7: 130,479,512 (GRCm39) I10N probably benign Het
Prss29 A G 17: 25,540,084 (GRCm39) T161A possibly damaging Het
Psmb5 C A 14: 54,854,130 (GRCm39) R116L probably damaging Het
Rsf1 A AGGGCGACGG 7: 97,229,111 (GRCm39) probably null Het
Secisbp2 C T 13: 51,833,923 (GRCm39) H688Y probably damaging Het
Senp5 A G 16: 31,802,665 (GRCm39) Y508H probably damaging Het
Shc3 T A 13: 51,605,651 (GRCm39) T210S possibly damaging Het
Slc27a2 G A 2: 126,429,800 (GRCm39) V467M probably damaging Het
Slc27a5 T A 7: 12,724,899 (GRCm39) E487V possibly damaging Het
Snx1 T C 9: 66,001,930 (GRCm39) T298A possibly damaging Het
Trir A G 8: 85,753,643 (GRCm39) D39G possibly damaging Het
Ubd C T 17: 37,506,242 (GRCm39) Q43* probably null Het
Ube2o T C 11: 116,432,194 (GRCm39) E924G probably damaging Het
Xirp2 C A 2: 67,346,425 (GRCm39) R2889S probably benign Het
Zfp804b T C 5: 6,820,534 (GRCm39) E843G probably benign Het
Other mutations in Vps13a
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00465:Vps13a APN 19 16,729,539 (GRCm39) missense probably damaging 0.98
IGL00537:Vps13a APN 19 16,657,409 (GRCm39) missense probably benign 0.03
IGL00562:Vps13a APN 19 16,712,078 (GRCm39) critical splice donor site probably null
IGL00563:Vps13a APN 19 16,712,078 (GRCm39) critical splice donor site probably null
IGL00579:Vps13a APN 19 16,684,726 (GRCm39) missense probably benign 0.29
IGL00662:Vps13a APN 19 16,681,904 (GRCm39) missense probably damaging 0.96
IGL00667:Vps13a APN 19 16,737,040 (GRCm39) missense probably damaging 1.00
IGL01102:Vps13a APN 19 16,628,781 (GRCm39) critical splice donor site probably null
IGL01139:Vps13a APN 19 16,617,989 (GRCm39) missense probably damaging 0.99
IGL01142:Vps13a APN 19 16,664,479 (GRCm39) missense possibly damaging 0.86
IGL01361:Vps13a APN 19 16,720,371 (GRCm39) missense probably damaging 1.00
IGL01386:Vps13a APN 19 16,678,516 (GRCm39) missense possibly damaging 0.87
IGL01593:Vps13a APN 19 16,739,545 (GRCm39) missense probably damaging 0.98
IGL01700:Vps13a APN 19 16,722,221 (GRCm39) nonsense probably null
IGL01767:Vps13a APN 19 16,641,258 (GRCm39) missense probably damaging 1.00
IGL01782:Vps13a APN 19 16,731,701 (GRCm39) missense probably damaging 0.98
IGL01808:Vps13a APN 19 16,687,650 (GRCm39) missense probably damaging 1.00
IGL01812:Vps13a APN 19 16,692,424 (GRCm39) missense probably benign
IGL01829:Vps13a APN 19 16,596,807 (GRCm39) missense probably benign 0.01
IGL01893:Vps13a APN 19 16,641,139 (GRCm39) missense probably damaging 1.00
IGL02222:Vps13a APN 19 16,659,539 (GRCm39) missense probably benign 0.06
IGL02295:Vps13a APN 19 16,692,406 (GRCm39) splice site probably benign
IGL02465:Vps13a APN 19 16,688,305 (GRCm39) missense probably benign 0.11
IGL02492:Vps13a APN 19 16,625,001 (GRCm39) missense probably damaging 1.00
IGL02581:Vps13a APN 19 16,632,686 (GRCm39) missense probably benign 0.41
IGL02633:Vps13a APN 19 16,697,772 (GRCm39) missense possibly damaging 0.82
IGL02641:Vps13a APN 19 16,676,185 (GRCm39) missense probably benign 0.01
IGL02659:Vps13a APN 19 16,630,063 (GRCm39) missense probably damaging 1.00
IGL02827:Vps13a APN 19 16,618,998 (GRCm39) missense possibly damaging 0.91
IGL02943:Vps13a APN 19 16,641,250 (GRCm39) missense probably damaging 1.00
IGL03057:Vps13a APN 19 16,646,058 (GRCm39) missense probably damaging 1.00
IGL03077:Vps13a APN 19 16,688,246 (GRCm39) missense probably benign
IGL03184:Vps13a APN 19 16,631,734 (GRCm39) missense probably benign 0.00
eggs UTSW 19 16,678,529 (GRCm39) missense probably damaging 1.00
excambio UTSW 19 16,723,311 (GRCm39) splice site probably null
Faster UTSW 19 16,596,849 (GRCm39) missense probably damaging 1.00
Ham UTSW 19 16,655,333 (GRCm39) missense probably benign 0.08
interchange UTSW 19 16,646,054 (GRCm39) missense probably damaging 1.00
PIT4377001:Vps13a UTSW 19 16,718,265 (GRCm39) missense probably damaging 1.00
R0045:Vps13a UTSW 19 16,618,174 (GRCm39) nonsense probably null
R0045:Vps13a UTSW 19 16,618,174 (GRCm39) nonsense probably null
R0048:Vps13a UTSW 19 16,653,504 (GRCm39) missense probably damaging 1.00
R0062:Vps13a UTSW 19 16,646,054 (GRCm39) missense probably damaging 1.00
R0062:Vps13a UTSW 19 16,646,054 (GRCm39) missense probably damaging 1.00
R0107:Vps13a UTSW 19 16,669,188 (GRCm39) missense probably benign 0.03
R0135:Vps13a UTSW 19 16,758,129 (GRCm39) missense probably damaging 1.00
R0138:Vps13a UTSW 19 16,637,863 (GRCm39) missense possibly damaging 0.95
R0346:Vps13a UTSW 19 16,655,333 (GRCm39) missense probably benign 0.08
R0359:Vps13a UTSW 19 16,618,941 (GRCm39) missense probably damaging 0.99
R0530:Vps13a UTSW 19 16,632,570 (GRCm39) splice site probably benign
R0541:Vps13a UTSW 19 16,681,941 (GRCm39) missense probably benign 0.00
R0614:Vps13a UTSW 19 16,630,058 (GRCm39) missense probably damaging 1.00
R0685:Vps13a UTSW 19 16,758,105 (GRCm39) missense probably damaging 1.00
R0801:Vps13a UTSW 19 16,664,020 (GRCm39) splice site probably benign
R0835:Vps13a UTSW 19 16,712,246 (GRCm39) splice site probably null
R0848:Vps13a UTSW 19 16,676,261 (GRCm39) missense probably damaging 1.00
R1114:Vps13a UTSW 19 16,727,515 (GRCm39) missense probably benign 0.41
R1205:Vps13a UTSW 19 16,617,905 (GRCm39) missense probably damaging 1.00
R1365:Vps13a UTSW 19 16,596,810 (GRCm39) missense probably damaging 1.00
R1445:Vps13a UTSW 19 16,678,602 (GRCm39) nonsense probably null
R1451:Vps13a UTSW 19 16,688,228 (GRCm39) missense probably benign 0.01
R1479:Vps13a UTSW 19 16,727,478 (GRCm39) splice site probably benign
R1533:Vps13a UTSW 19 16,678,494 (GRCm39) nonsense probably null
R1600:Vps13a UTSW 19 16,643,636 (GRCm39) missense probably benign 0.01
R1870:Vps13a UTSW 19 16,737,316 (GRCm39) missense probably damaging 1.00
R1871:Vps13a UTSW 19 16,642,028 (GRCm39) missense probably benign 0.01
R1959:Vps13a UTSW 19 16,655,302 (GRCm39) missense possibly damaging 0.49
R1960:Vps13a UTSW 19 16,702,995 (GRCm39) missense probably damaging 1.00
R1993:Vps13a UTSW 19 16,699,822 (GRCm39) missense probably benign 0.07
R2257:Vps13a UTSW 19 16,659,538 (GRCm39) missense possibly damaging 0.85
R2276:Vps13a UTSW 19 16,687,790 (GRCm39) missense possibly damaging 0.47
R2326:Vps13a UTSW 19 16,720,421 (GRCm39) missense possibly damaging 0.71
R2338:Vps13a UTSW 19 16,697,817 (GRCm39) missense probably damaging 1.00
R2359:Vps13a UTSW 19 16,630,043 (GRCm39) splice site probably benign
R2421:Vps13a UTSW 19 16,737,035 (GRCm39) missense probably benign
R2847:Vps13a UTSW 19 16,680,963 (GRCm39) missense probably damaging 0.98
R3081:Vps13a UTSW 19 16,642,101 (GRCm39) missense probably benign 0.02
R3522:Vps13a UTSW 19 16,743,857 (GRCm39) splice site probably benign
R3613:Vps13a UTSW 19 16,662,766 (GRCm39) missense probably damaging 1.00
R3797:Vps13a UTSW 19 16,723,311 (GRCm39) splice site probably null
R3874:Vps13a UTSW 19 16,722,317 (GRCm39) missense probably benign 0.01
R4032:Vps13a UTSW 19 16,594,263 (GRCm39) missense probably damaging 1.00
R4111:Vps13a UTSW 19 16,617,992 (GRCm39) missense probably damaging 1.00
R4383:Vps13a UTSW 19 16,678,529 (GRCm39) missense probably damaging 1.00
R4504:Vps13a UTSW 19 16,672,866 (GRCm39) missense possibly damaging 0.93
R4578:Vps13a UTSW 19 16,659,474 (GRCm39) missense probably damaging 0.98
R4587:Vps13a UTSW 19 16,617,403 (GRCm39) missense probably damaging 1.00
R4588:Vps13a UTSW 19 16,617,403 (GRCm39) missense probably damaging 1.00
R4605:Vps13a UTSW 19 16,617,403 (GRCm39) missense probably damaging 1.00
R4714:Vps13a UTSW 19 16,727,220 (GRCm39) missense probably benign 0.01
R4756:Vps13a UTSW 19 16,632,580 (GRCm39) missense probably benign 0.01
R4831:Vps13a UTSW 19 16,655,356 (GRCm39) missense probably benign 0.04
R5068:Vps13a UTSW 19 16,723,422 (GRCm39) missense probably benign 0.01
R5070:Vps13a UTSW 19 16,631,848 (GRCm39) missense probably benign
R5082:Vps13a UTSW 19 16,722,257 (GRCm39) missense probably damaging 1.00
R5182:Vps13a UTSW 19 16,672,863 (GRCm39) missense possibly damaging 0.81
R5189:Vps13a UTSW 19 16,662,679 (GRCm39) missense probably damaging 1.00
R5283:Vps13a UTSW 19 16,655,334 (GRCm39) missense probably damaging 0.96
R5294:Vps13a UTSW 19 16,619,031 (GRCm39) missense probably damaging 1.00
R5304:Vps13a UTSW 19 16,687,751 (GRCm39) missense possibly damaging 0.78
R5554:Vps13a UTSW 19 16,699,775 (GRCm39) missense probably damaging 1.00
R5592:Vps13a UTSW 19 16,702,935 (GRCm39) missense probably damaging 1.00
R5611:Vps13a UTSW 19 16,702,936 (GRCm39) missense probably damaging 1.00
R5665:Vps13a UTSW 19 16,646,054 (GRCm39) missense probably damaging 1.00
R5671:Vps13a UTSW 19 16,692,464 (GRCm39) missense probably benign 0.03
R5684:Vps13a UTSW 19 16,676,409 (GRCm39) missense probably benign 0.00
R5767:Vps13a UTSW 19 16,641,928 (GRCm39) missense probably damaging 1.00
R5810:Vps13a UTSW 19 16,643,688 (GRCm39) missense probably benign 0.00
R5866:Vps13a UTSW 19 16,657,387 (GRCm39) missense probably benign 0.04
R5886:Vps13a UTSW 19 16,641,926 (GRCm39) missense probably benign 0.01
R5933:Vps13a UTSW 19 16,637,894 (GRCm39) missense probably benign 0.34
R5965:Vps13a UTSW 19 16,596,392 (GRCm39) splice site probably null
R6259:Vps13a UTSW 19 16,664,534 (GRCm39) nonsense probably null
R6459:Vps13a UTSW 19 16,641,382 (GRCm39) missense possibly damaging 0.56
R6485:Vps13a UTSW 19 16,657,414 (GRCm39) missense probably damaging 0.99
R6520:Vps13a UTSW 19 16,702,943 (GRCm39) missense probably damaging 1.00
R6644:Vps13a UTSW 19 16,722,283 (GRCm39) missense possibly damaging 0.90
R6932:Vps13a UTSW 19 16,655,439 (GRCm39) missense probably benign 0.01
R6934:Vps13a UTSW 19 16,653,558 (GRCm39) missense probably damaging 1.00
R6951:Vps13a UTSW 19 16,701,104 (GRCm39) missense probably benign 0.00
R7027:Vps13a UTSW 19 16,642,028 (GRCm39) missense probably benign 0.01
R7126:Vps13a UTSW 19 16,688,243 (GRCm39) missense probably benign
R7206:Vps13a UTSW 19 16,731,662 (GRCm39) missense probably damaging 1.00
R7248:Vps13a UTSW 19 16,655,406 (GRCm39) missense probably benign 0.25
R7252:Vps13a UTSW 19 16,638,428 (GRCm39) missense probably benign 0.00
R7255:Vps13a UTSW 19 16,631,703 (GRCm39) critical splice donor site probably null
R7382:Vps13a UTSW 19 16,596,849 (GRCm39) missense probably damaging 1.00
R7422:Vps13a UTSW 19 16,727,537 (GRCm39) missense probably damaging 1.00
R7425:Vps13a UTSW 19 16,701,066 (GRCm39) missense probably benign 0.13
R7523:Vps13a UTSW 19 16,681,153 (GRCm39) missense probably benign
R7586:Vps13a UTSW 19 16,624,962 (GRCm39) missense probably benign 0.08
R7587:Vps13a UTSW 19 16,681,153 (GRCm39) missense probably benign 0.00
R7593:Vps13a UTSW 19 16,703,027 (GRCm39) missense probably damaging 1.00
R7637:Vps13a UTSW 19 16,727,513 (GRCm39) missense probably benign 0.02
R7763:Vps13a UTSW 19 16,723,364 (GRCm39) missense possibly damaging 0.95
R7813:Vps13a UTSW 19 16,628,820 (GRCm39) missense possibly damaging 0.81
R7815:Vps13a UTSW 19 16,702,936 (GRCm39) missense probably damaging 1.00
R7861:Vps13a UTSW 19 16,632,668 (GRCm39) missense probably damaging 1.00
R7909:Vps13a UTSW 19 16,697,794 (GRCm39) nonsense probably null
R7939:Vps13a UTSW 19 16,718,155 (GRCm39) missense possibly damaging 0.94
R8108:Vps13a UTSW 19 16,618,151 (GRCm39) missense probably damaging 1.00
R8123:Vps13a UTSW 19 16,625,066 (GRCm39) missense probably benign 0.01
R8134:Vps13a UTSW 19 16,631,718 (GRCm39) missense possibly damaging 0.71
R8168:Vps13a UTSW 19 16,726,912 (GRCm39) missense probably benign 0.09
R8272:Vps13a UTSW 19 16,727,209 (GRCm39) critical splice donor site probably null
R8293:Vps13a UTSW 19 16,645,969 (GRCm39) missense possibly damaging 0.81
R8303:Vps13a UTSW 19 16,594,270 (GRCm39) missense probably benign 0.00
R8383:Vps13a UTSW 19 16,701,069 (GRCm39) missense possibly damaging 0.83
R8386:Vps13a UTSW 19 16,678,483 (GRCm39) critical splice donor site probably null
R8433:Vps13a UTSW 19 16,718,600 (GRCm39) missense possibly damaging 0.56
R8436:Vps13a UTSW 19 16,718,157 (GRCm39) missense probably benign 0.10
R8450:Vps13a UTSW 19 16,631,871 (GRCm39) splice site probably null
R8476:Vps13a UTSW 19 16,699,821 (GRCm39) missense possibly damaging 0.60
R8501:Vps13a UTSW 19 16,659,484 (GRCm39) missense probably benign 0.39
R8552:Vps13a UTSW 19 16,731,684 (GRCm39) missense probably damaging 0.99
R8680:Vps13a UTSW 19 16,623,270 (GRCm39) missense possibly damaging 0.84
R8784:Vps13a UTSW 19 16,642,153 (GRCm39) missense probably damaging 1.00
R8871:Vps13a UTSW 19 16,641,186 (GRCm39) missense probably damaging 1.00
R8945:Vps13a UTSW 19 16,642,114 (GRCm39) missense probably damaging 1.00
R8948:Vps13a UTSW 19 16,723,340 (GRCm39) missense probably damaging 0.99
R8950:Vps13a UTSW 19 16,723,340 (GRCm39) missense probably damaging 0.99
R8960:Vps13a UTSW 19 16,683,247 (GRCm39) missense possibly damaging 0.67
R9189:Vps13a UTSW 19 16,663,961 (GRCm39) missense probably benign
R9366:Vps13a UTSW 19 16,672,894 (GRCm39) missense probably damaging 1.00
R9505:Vps13a UTSW 19 16,719,908 (GRCm39) missense possibly damaging 0.94
R9601:Vps13a UTSW 19 16,623,337 (GRCm39) missense possibly damaging 0.84
R9735:Vps13a UTSW 19 16,701,111 (GRCm39) missense probably damaging 1.00
R9776:Vps13a UTSW 19 16,736,958 (GRCm39) missense probably benign
R9796:Vps13a UTSW 19 16,631,828 (GRCm39) missense probably benign 0.01
X0061:Vps13a UTSW 19 16,623,232 (GRCm39) missense probably benign 0.40
X0066:Vps13a UTSW 19 16,719,917 (GRCm39) missense probably benign 0.33
Z1177:Vps13a UTSW 19 16,676,477 (GRCm39) critical splice acceptor site probably null
Z31818:Vps13a UTSW 19 16,758,118 (GRCm39) missense possibly damaging 0.94
Predicted Primers PCR Primer
(F):5'- TCACTTCATTCGTGGGAACTAC -3'
(R):5'- CACTTGTAGCATTTACTGGGACC -3'

Sequencing Primer
(F):5'- ATTCGTGGGAACTACTTTTTCAC -3'
(R):5'- AATGGAAACCTCATGATATGTGC -3'
Posted On 2018-04-27