Incidental Mutation 'R1600:Vps13a'
ID 176117
Institutional Source Beutler Lab
Gene Symbol Vps13a
Ensembl Gene ENSMUSG00000046230
Gene Name vacuolar protein sorting 13A
Synonyms 4930543C13Rik, D330038K10Rik, 4930516E05Rik
MMRRC Submission 039637-MU
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R1600 (G1)
Quality Score 225
Status Validated
Chromosome 19
Chromosomal Location 16592730-16758297 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 16643636 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Asparagine to Serine at position 2080 (N2080S)
Ref Sequence ENSEMBL: ENSMUSP00000153129 (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: N2080S

PolyPhen 2 Score 0.002 (Sensitivity: 0.99; Specificity: 0.30)
SMART Domains Protein: ENSMUSP00000068716
Gene: ENSMUSG00000046230
AA Change: N2080S

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 probably benign
Transcript: ENSMUST00000224149
AA Change: N2080S

PolyPhen 2 Score 0.009 (Sensitivity: 0.96; Specificity: 0.77)
Predicted Effect noncoding transcript
Transcript: ENSMUST00000224725
Predicted Effect probably benign
Transcript: ENSMUST00000225233
Meta Mutation Damage Score 0.0580 question?
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.4%
  • 10x: 96.6%
  • 20x: 93.6%
Validation Efficiency 85% (41/48)
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: 39 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Acin1 T C 14: 54,881,174 (GRCm39) probably benign Het
Acot3 C T 12: 84,105,484 (GRCm39) A317V probably benign Het
Ahrr T C 13: 74,362,497 (GRCm39) D334G probably benign Het
Alpk2 C T 18: 65,511,108 (GRCm39) V30M probably damaging Het
Arhgef25 G T 10: 127,021,158 (GRCm39) H281N probably damaging Het
B3gntl1 A G 11: 121,521,662 (GRCm39) M175T probably damaging Het
Brca2 T A 5: 150,484,295 (GRCm39) probably benign Het
Ccnj A T 19: 40,833,101 (GRCm39) probably benign Het
Cebpzos A G 17: 79,225,817 (GRCm39) K11E probably damaging Het
Col6a6 A G 9: 105,655,274 (GRCm39) S816P probably damaging Het
Cul4a A G 8: 13,173,954 (GRCm39) R64G probably damaging Het
Cul7 C A 17: 46,962,748 (GRCm39) C126* probably null Het
Ercc2 T C 7: 19,119,866 (GRCm39) Y176H probably benign Het
Frem2 T G 3: 53,455,144 (GRCm39) D2144A probably damaging Het
Gabrg3 A T 7: 56,384,822 (GRCm39) Y246* probably null Het
Gpatch2l T C 12: 86,303,708 (GRCm39) probably null Het
Grk1 A G 8: 13,455,406 (GRCm39) T97A probably benign Het
Hmcn2 A G 2: 31,320,799 (GRCm39) E4004G probably damaging Het
Kcnu1 A T 8: 26,339,821 (GRCm39) R46S probably damaging Het
Lrrfip1 T C 1: 91,042,389 (GRCm39) S265P probably damaging Het
Lyve1 A G 7: 110,452,902 (GRCm39) probably null Het
Mme A G 3: 63,272,479 (GRCm39) Y659C probably damaging Het
Mrs2 G T 13: 25,179,393 (GRCm39) N299K possibly damaging Het
Mtnr1b T C 9: 15,774,615 (GRCm39) Y148C probably damaging Het
Myo5b T A 18: 74,846,611 (GRCm39) probably benign Het
Neb A G 2: 52,161,616 (GRCm39) Y2059H probably damaging Het
Nkain3 T C 4: 20,469,528 (GRCm39) probably benign Het
Peg10 A T 6: 4,757,080 (GRCm39) probably benign Het
Pramel20 A G 4: 143,298,537 (GRCm39) E160G possibly damaging Het
Rufy2 A G 10: 62,842,450 (GRCm39) T458A probably benign Het
Sec14l1 G A 11: 117,041,430 (GRCm39) V448I probably benign Het
Tbx19 C T 1: 164,970,136 (GRCm39) G251D possibly damaging Het
Tcstv7b T C 13: 120,702,369 (GRCm39) V55A probably benign Het
Trappc9 G A 15: 72,808,958 (GRCm39) Q711* probably null Het
Trpm3 A G 19: 22,116,519 (GRCm39) R13G probably benign Het
Usp33 G T 3: 152,085,247 (GRCm39) A628S probably damaging Het
Wdr45b A T 11: 121,221,015 (GRCm39) I221N probably damaging Het
Zfp119a A T 17: 56,175,355 (GRCm39) W47R possibly damaging Het
Zswim9 A G 7: 13,003,497 (GRCm39) C118R probably damaging 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
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'- CCCGTTACTAAGCAATGCTGCAACCTC -3'
(R):5'- AAGCCACTGCCACCTGGCCTAATTTC -3'

Sequencing Primer
(F):5'- GCAATGCTGCAACCTCTGTTAC -3'
(R):5'- ACCTGGCCTAATTTCAGGTCTC -3'
Posted On 2014-04-24