Incidental Mutation 'R1114:Vps13a'
ID 97095
Institutional Source Beutler Lab
Gene Symbol Vps13a
Ensembl Gene ENSMUSG00000046230
Gene Name vacuolar protein sorting 13A
Synonyms 4930543C13Rik, D330038K10Rik, 4930516E05Rik
MMRRC Submission 039187-MU
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R1114 (G1)
Quality Score 225
Status Validated
Chromosome 19
Chromosomal Location 16592730-16758297 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) G to T at 16727515 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Histidine to Asparagine at position 196 (H196N)
Ref Sequence ENSEMBL: ENSMUSP00000068716 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000068156] [ENSMUST00000224149]
AlphaFold no structure available at present
Predicted Effect probably benign
Transcript: ENSMUST00000068156
AA Change: H196N

PolyPhen 2 Score 0.408 (Sensitivity: 0.89; Specificity: 0.90)
SMART Domains Protein: ENSMUSP00000068716
Gene: ENSMUSG00000046230
AA Change: H196N

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: ENSMUST00000223846
Predicted Effect probably benign
Transcript: ENSMUST00000224149
AA Change: H196N

PolyPhen 2 Score 0.081 (Sensitivity: 0.93; Specificity: 0.85)
Predicted Effect noncoding transcript
Transcript: ENSMUST00000224428
Predicted Effect noncoding transcript
Transcript: ENSMUST00000225764
Meta Mutation Damage Score 0.0749 question?
Coding Region Coverage
  • 1x: 98.7%
  • 3x: 97.5%
  • 10x: 93.5%
  • 20x: 84.2%
Validation Efficiency 100% (47/47)
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: 41 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
1700128F08Rik T A 9: 8,222,179 (GRCm39) noncoding transcript Het
Acss3 T A 10: 106,824,740 (GRCm39) R422S possibly damaging Het
Asb15 G A 6: 24,567,176 (GRCm39) R499H probably damaging Het
Aspm C T 1: 139,389,662 (GRCm39) probably benign Het
Camk2d G A 3: 126,633,941 (GRCm39) V488M probably damaging Het
Cd247 A G 1: 165,616,407 (GRCm39) K4E probably benign Het
Cdh20 A G 1: 104,906,739 (GRCm39) D522G probably damaging Het
Cse1l T A 2: 166,783,123 (GRCm39) probably benign Het
Dctn2 T A 10: 127,114,011 (GRCm39) probably null Het
Dpy19l1 A T 9: 24,336,072 (GRCm39) F545I probably benign Het
Dpy19l4 A G 4: 11,287,643 (GRCm39) probably benign Het
Dsg4 A T 18: 20,599,540 (GRCm39) T719S possibly damaging Het
Dusp12 A C 1: 170,708,586 (GRCm39) V48G probably damaging Het
Efcab7 A T 4: 99,735,452 (GRCm39) R159* probably null Het
Fabp3 C T 4: 130,206,180 (GRCm39) T57I probably benign Het
Fbxw20 A G 9: 109,052,550 (GRCm39) V261A probably damaging Het
Gtf3c3 C T 1: 54,456,937 (GRCm39) A488T probably damaging Het
Inpp5j C A 11: 3,444,814 (GRCm39) R953L possibly damaging Het
Itprid2 A G 2: 79,487,873 (GRCm39) E652G probably damaging Het
Lrrk2 C T 15: 91,584,671 (GRCm39) R363* probably null Het
Ltbp1 A G 17: 75,667,770 (GRCm39) D1089G probably benign Het
Luc7l T C 17: 26,494,832 (GRCm39) probably benign Het
Mdn1 G A 4: 32,746,568 (GRCm39) probably null Het
Mgat4a A T 1: 37,503,487 (GRCm39) probably benign Het
Mmp12 A G 9: 7,358,289 (GRCm39) T392A possibly damaging Het
Nlrp12 A G 7: 3,277,166 (GRCm39) V921A probably benign Het
Or5m5 A T 2: 85,814,651 (GRCm39) I156F probably benign Het
Or5t7 G A 2: 86,507,629 (GRCm39) T16I possibly damaging Het
Or6c8b T A 10: 128,882,711 (GRCm39) I74F possibly damaging Het
Pkd2l1 T C 19: 44,179,983 (GRCm39) probably benign Het
Pramel24 A G 4: 143,453,425 (GRCm39) I178V probably benign Het
Rictor C A 15: 6,823,486 (GRCm39) C1554* probably null Het
Ryr2 A G 13: 11,960,867 (GRCm39) C24R probably damaging Het
Scamp2 T A 9: 57,488,863 (GRCm39) I188N probably damaging Het
Smg1 A T 7: 117,759,013 (GRCm39) probably benign Het
Sned1 G A 1: 93,209,376 (GRCm39) V830M possibly damaging Het
Synrg C A 11: 83,914,262 (GRCm39) probably benign Het
Syt9 G T 7: 107,024,562 (GRCm39) V152F possibly damaging Het
Trmt2a A G 16: 18,068,304 (GRCm39) probably benign Het
Vmn2r100 T C 17: 19,752,261 (GRCm39) I831T probably damaging Het
Xdh T C 17: 74,248,144 (GRCm39) 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
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
R6346:Vps13a UTSW 19 16,659,578 (GRCm39) missense possibly damaging 0.94
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'- CATCTCAGAGTTCACATTCCAGTAAGCAAA -3'
(R):5'- GCTAACAGAACCTACTCTATTGTCTTGCC -3'

Sequencing Primer
(F):5'- ACATTCCAGTAAGCAAAGAGATTATC -3'
(R):5'- GACCAGTGAGTTCTTTGAAAGC -3'
Posted On 2014-01-05