Incidental Mutation 'R9460:Vipas39'
ID 714826
Institutional Source Beutler Lab
Gene Symbol Vipas39
Ensembl Gene ENSMUSG00000021038
Gene Name VPS33B interacting protein, apical-basolateral polarity regulator, spe-39 homolog
Synonyms Vipar, SPE-39
MMRRC Submission
Accession Numbers
Essential gene? Possibly essential (E-score: 0.606) question?
Stock # R9460 (G1)
Quality Score 225.009
Status Validated
Chromosome 12
Chromosomal Location 87285642-87313030 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 87288021 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Leucine to Proline at position 482 (L482P)
Ref Sequence ENSEMBL: ENSMUSP00000072527 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000021426] [ENSMUST00000072744] [ENSMUST00000179379] [ENSMUST00000221768] [ENSMUST00000222480]
AlphaFold Q8BGQ1
Predicted Effect probably damaging
Transcript: ENSMUST00000021426
AA Change: L463P

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000021426
Gene: ENSMUSG00000021038
AA Change: L463P

DomainStartEndE-ValueType
Pfam:Golgin_A5 24 470 4.3e-147 PFAM
Predicted Effect probably damaging
Transcript: ENSMUST00000072744
AA Change: L482P

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000072527
Gene: ENSMUSG00000021038
AA Change: L482P

DomainStartEndE-ValueType
Pfam:Golgin_A5 24 489 3.7e-154 PFAM
Predicted Effect probably damaging
Transcript: ENSMUST00000179379
AA Change: L463P

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000137190
Gene: ENSMUSG00000021038
AA Change: L463P

DomainStartEndE-ValueType
Pfam:Golgin_A5 24 470 4.3e-147 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000221768
Predicted Effect probably benign
Transcript: ENSMUST00000222480
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 100.0%
  • 10x: 99.8%
  • 20x: 99.3%
Validation Efficiency 100% (56/56)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a protein involved in the sorting of lysosomal proteins. Mutations in this gene are associated with ARCS2 (arthrogryposis, renal dysfunction, and cholestasis-2). Alternative splicing results in multiple transcript variants.[provided by RefSeq, Jul 2010]
PHENOTYPE: Mice homozygous for a conditional allele activated by an inducible cre exhibit dry and scaly skin, hair loss, and defects in tail tendon collagen I structure. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 58 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Acsbg3 C T 17: 57,183,316 (GRCm39) T19I probably damaging Het
Alg1 T A 16: 5,060,425 (GRCm39) M382K probably damaging Het
Arhgap17 A G 7: 122,879,286 (GRCm39) S822P unknown Het
Bend7 A C 2: 4,749,302 (GRCm39) T140P probably benign Het
C1rb T G 6: 124,557,865 (GRCm39) D667E probably benign Het
Carmil1 A G 13: 24,253,750 (GRCm39) C794R probably damaging Het
Cd36 T C 5: 18,000,608 (GRCm39) D365G probably null Het
Cep164 T C 9: 45,685,282 (GRCm39) N825S probably benign Het
Cp T C 3: 20,018,566 (GRCm39) L90P Het
Cpeb2 C T 5: 43,390,769 (GRCm39) probably benign Het
Cramp1 A G 17: 25,222,281 (GRCm39) S146P probably damaging Het
Csmd3 A T 15: 47,617,130 (GRCm39) D1019E Het
Cyp2d10 T A 15: 82,289,470 (GRCm39) D214V probably benign Het
Dcaf17 G C 2: 70,917,695 (GRCm39) V406L possibly damaging Het
Ehmt1 A G 2: 24,728,791 (GRCm39) V703A probably benign Het
Ermp1 A C 19: 29,609,916 (GRCm39) V293G probably benign Het
Fancd2os C A 6: 113,574,569 (GRCm39) V146F probably benign Het
Galnt12 C T 4: 47,117,983 (GRCm39) T426I probably damaging Het
Gm11011 T A 2: 169,429,289 (GRCm39) T44S unknown Het
Gm2832 C T 14: 41,000,843 (GRCm39) T27I Het
Klhl32 A G 4: 24,649,866 (GRCm39) V310A probably benign Het
Kntc1 T A 5: 123,941,378 (GRCm39) C1728* probably null Het
Lama2 T A 10: 27,298,475 (GRCm39) N207I probably damaging Het
Lpar5 A G 6: 125,058,234 (GRCm39) probably benign Het
Map3k8 T C 18: 4,349,277 (GRCm39) I14V probably benign Het
Marf1 A T 16: 13,947,526 (GRCm39) V1151E probably damaging Het
Me1 G A 9: 86,495,685 (GRCm39) A274V probably damaging Het
Mybpc1 A T 10: 88,372,197 (GRCm39) I797N probably damaging Het
Myo15a T A 11: 60,372,566 (GRCm39) probably null Het
N4bp2 A T 5: 65,963,886 (GRCm39) D645V probably benign Het
Nlrp4f G T 13: 65,342,006 (GRCm39) D546E possibly damaging Het
Npc1 T C 18: 12,346,398 (GRCm39) D266G possibly damaging Het
Or4a81 G A 2: 89,618,778 (GRCm39) S306L probably benign Het
Or8k16 A G 2: 85,520,359 (GRCm39) I195M probably benign Het
Pcdha12 C T 18: 37,153,574 (GRCm39) R98W probably damaging Het
Peg10 GC GCTCC 6: 4,756,452 (GRCm39) probably benign Het
Pigr T C 1: 130,772,403 (GRCm39) I207T probably damaging Het
Plxnc1 T A 10: 94,700,895 (GRCm39) E596D probably benign Het
Polr1e C T 4: 45,018,691 (GRCm39) P7L probably benign Het
Ppp5c G T 7: 16,741,137 (GRCm39) Y313* probably null Het
Sacs C A 14: 61,441,611 (GRCm39) T1219K probably benign Het
Scn3a A G 2: 65,300,535 (GRCm39) V1277A probably damaging Het
Serinc5 G T 13: 92,844,607 (GRCm39) A450S possibly damaging Het
Serinc5 T C 13: 92,844,619 (GRCm39) C454R probably benign Het
Slc12a6 G A 2: 112,183,280 (GRCm39) V771I probably benign Het
Slc4a1ap T C 5: 31,685,463 (GRCm39) I247T probably benign Het
Snx10 T A 6: 51,565,888 (GRCm39) S184R probably damaging Het
Tgm2 A T 2: 157,971,241 (GRCm39) probably null Het
Thap1 CAGCATCTGCTCGGAGCA CAGCA 8: 26,650,884 (GRCm39) probably null Het
Thsd7b T C 1: 130,090,674 (GRCm39) probably null Het
Tiam2 G A 17: 3,487,585 (GRCm39) G702E probably damaging Het
Tmco4 T A 4: 138,747,387 (GRCm39) V212D probably damaging Het
Usp48 G A 4: 137,340,996 (GRCm39) G332E probably benign Het
Vmn1r5 T A 6: 56,962,829 (GRCm39) M168K Het
Vps13c T C 9: 67,837,904 (GRCm39) L1818S possibly damaging Het
Vwa2 A G 19: 56,886,388 (GRCm39) I152V probably benign Het
Zfp180 G A 7: 23,804,399 (GRCm39) G273R probably damaging Het
Zpld2 G A 4: 133,929,312 (GRCm39) P331L probably benign Het
Other mutations in Vipas39
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL01413:Vipas39 APN 12 87,296,171 (GRCm39) missense probably benign 0.03
IGL01418:Vipas39 APN 12 87,296,171 (GRCm39) missense probably benign 0.03
IGL02026:Vipas39 APN 12 87,298,483 (GRCm39) splice site probably benign
IGL03089:Vipas39 APN 12 87,300,028 (GRCm39) missense probably damaging 1.00
R0173:Vipas39 UTSW 12 87,297,285 (GRCm39) splice site probably benign
R0909:Vipas39 UTSW 12 87,288,105 (GRCm39) missense probably benign 0.21
R1505:Vipas39 UTSW 12 87,292,934 (GRCm39) missense probably damaging 1.00
R2897:Vipas39 UTSW 12 87,289,297 (GRCm39) missense possibly damaging 0.78
R2968:Vipas39 UTSW 12 87,289,345 (GRCm39) missense probably benign 0.45
R2969:Vipas39 UTSW 12 87,289,345 (GRCm39) missense probably benign 0.45
R2970:Vipas39 UTSW 12 87,289,345 (GRCm39) missense probably benign 0.45
R4622:Vipas39 UTSW 12 87,291,317 (GRCm39) missense probably damaging 1.00
R4676:Vipas39 UTSW 12 87,288,075 (GRCm39) missense probably damaging 1.00
R5181:Vipas39 UTSW 12 87,286,601 (GRCm39) missense probably damaging 1.00
R5188:Vipas39 UTSW 12 87,301,021 (GRCm39) missense probably benign 0.21
R5881:Vipas39 UTSW 12 87,298,581 (GRCm39) nonsense probably null
R6080:Vipas39 UTSW 12 87,288,727 (GRCm39) missense probably damaging 1.00
R6425:Vipas39 UTSW 12 87,288,063 (GRCm39) missense probably damaging 0.98
R6896:Vipas39 UTSW 12 87,289,345 (GRCm39) missense probably benign 0.45
R7438:Vipas39 UTSW 12 87,288,705 (GRCm39) splice site probably null
R7538:Vipas39 UTSW 12 87,310,677 (GRCm39) critical splice donor site probably null
R8436:Vipas39 UTSW 12 87,304,191 (GRCm39) missense probably damaging 0.99
R8919:Vipas39 UTSW 12 87,305,858 (GRCm39) nonsense probably null
R9174:Vipas39 UTSW 12 87,305,885 (GRCm39) missense possibly damaging 0.89
R9671:Vipas39 UTSW 12 87,292,985 (GRCm39) missense probably benign 0.13
Predicted Primers PCR Primer
(F):5'- ATCACATGCTATCTACCTTGGG -3'
(R):5'- TCTTGAGCCCAGGAGCAAAG -3'

Sequencing Primer
(F):5'- CCTCCTAAGTGCTGGGATTAAAAGC -3'
(R):5'- CCCAGGAGCAAAGAAACCGTG -3'
Posted On 2022-06-15