Incidental Mutation 'R5219:Ap3d1'
ID 402232
Institutional Source Beutler Lab
Gene Symbol Ap3d1
Ensembl Gene ENSMUSG00000020198
Gene Name adaptor-related protein complex 3, delta 1 subunit
Synonyms mBLVR1, Bolvr
MMRRC Submission 042792-MU
Accession Numbers
Essential gene? Probably essential (E-score: 0.931) question?
Stock # R5219 (G1)
Quality Score 225
Status Validated
Chromosome 10
Chromosomal Location 80542790-80578098 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 80545651 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Glutamic Acid to Glycine at position 1026 (E1026G)
Ref Sequence ENSEMBL: ENSMUSP00000020420 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000020420] [ENSMUST00000218184] [ENSMUST00000218610]
AlphaFold O54774
Predicted Effect probably benign
Transcript: ENSMUST00000020420
AA Change: E1026G

PolyPhen 2 Score 0.029 (Sensitivity: 0.95; Specificity: 0.82)
SMART Domains Protein: ENSMUSP00000020420
Gene: ENSMUSG00000020198
AA Change: E1026G

DomainStartEndE-ValueType
Pfam:Adaptin_N 32 583 6.6e-153 PFAM
Pfam:Cnd1 130 292 2.1e-8 PFAM
low complexity region 629 642 N/A INTRINSIC
BLVR 660 803 5.3e-80 SMART
low complexity region 835 861 N/A INTRINSIC
low complexity region 871 881 N/A INTRINSIC
coiled coil region 910 933 N/A INTRINSIC
low complexity region 947 964 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000095426
SMART Domains Protein: ENSMUSP00000093076
Gene: ENSMUSG00000055862

DomainStartEndE-ValueType
Pfam:IZUMO 26 167 1.1e-31 PFAM
Predicted Effect noncoding transcript
Transcript: ENSMUST00000217823
Predicted Effect noncoding transcript
Transcript: ENSMUST00000218125
Predicted Effect probably benign
Transcript: ENSMUST00000218184
Predicted Effect probably benign
Transcript: ENSMUST00000218330
Predicted Effect noncoding transcript
Transcript: ENSMUST00000219816
Predicted Effect noncoding transcript
Transcript: ENSMUST00000218538
Predicted Effect noncoding transcript
Transcript: ENSMUST00000219422
Predicted Effect probably benign
Transcript: ENSMUST00000218610
Predicted Effect noncoding transcript
Transcript: ENSMUST00000219987
Predicted Effect noncoding transcript
Transcript: ENSMUST00000219986
Meta Mutation Damage Score 0.0898 question?
Coding Region Coverage
  • 1x: 99.3%
  • 3x: 98.7%
  • 10x: 97.4%
  • 20x: 95.7%
Validation Efficiency 97% (68/70)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The protein encoded by this gene is a subunit of the AP3 adaptor-like complex, which is not clathrin-associated, but is associated with the golgi region, as well as more peripheral structures. The AP-3 complex facilitates the budding of vesicles from the golgi membrane, and may be directly involved in trafficking to lysosomes. This subunit is implicated in intracellular biogenesis and trafficking of pigment granules, and possibly platelet dense granules and neurotransmitter vesicles. Defects in this gene are a cause of a new type of Hermansky-Pudlak syndrome. [provided by RefSeq, Feb 2017]
PHENOTYPE: Mutant mice show coat and eye color dilution, platelet defects, lysosomal abnormalities, inner ear degeneration and neurological defects and model Hermansky-Pudlak storage pool deficiency syndrome. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 62 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
1700063H04Rik A G 6: 122,369,299 (GRCm39) noncoding transcript Het
4933428M09Rik G T X: 138,080,282 (GRCm39) G16* probably null Het
A2m A G 6: 121,653,909 (GRCm39) H1414R possibly damaging Het
A530064D06Rik G T 17: 48,470,518 (GRCm39) D154E possibly damaging Het
Adam34 C T 8: 44,104,461 (GRCm39) D395N probably benign Het
Agl A G 3: 116,572,370 (GRCm39) V195A possibly damaging Het
Aip T C 19: 4,165,180 (GRCm39) I230V probably benign Het
Akap10 A C 11: 61,813,617 (GRCm39) S43A probably benign Het
Arid5b T A 10: 68,113,940 (GRCm39) K32N probably benign Het
Atp6v0a2 C A 5: 124,790,249 (GRCm39) N477K probably damaging Het
Atr A C 9: 95,763,291 (GRCm39) I1062L probably damaging Het
Ces2h T C 8: 105,743,278 (GRCm39) V171A probably damaging Het
Cnot2 A G 10: 116,342,215 (GRCm39) probably null Het
Cpne3 A T 4: 19,526,366 (GRCm39) L391H probably damaging Het
Ctdp1 A G 18: 80,490,675 (GRCm39) L715P probably damaging Het
Dcxr T C 11: 120,616,314 (GRCm39) probably benign Het
Dhtkd1 C T 2: 5,919,627 (GRCm39) A585T probably benign Het
Elapor2 G T 5: 9,511,486 (GRCm39) W949C probably damaging Het
Fcgbp G A 7: 27,803,510 (GRCm39) A1705T probably damaging Het
Galr1 A T 18: 82,412,110 (GRCm39) V252D probably damaging Het
Gm11677 A G 11: 111,616,225 (GRCm39) noncoding transcript Het
Gp6 A G 7: 4,371,998 (GRCm39) V252A possibly damaging Het
Inpp4b T C 8: 82,610,785 (GRCm39) V176A probably benign Het
Irx2 G C 13: 72,779,420 (GRCm39) A235P probably damaging Het
Klk1b11 G A 7: 43,649,120 (GRCm39) C219Y probably damaging Het
Lamc1 C A 1: 153,103,442 (GRCm39) V1375L probably damaging Het
Lars1 A T 18: 42,367,785 (GRCm39) V431E probably benign Het
Lmntd2 T C 7: 140,791,387 (GRCm39) probably null Het
Ltbp4 A T 7: 27,026,746 (GRCm39) W500R probably benign Het
Ltbp4 AATTCAGGCCAAGGCTGGGATTCAGGCCGAGGCCGGGATTCAGGCCTAGGCTGGGATTCAGGC AATTCAGGCCTAGGCTGGGATTCAGGC 7: 27,026,736 (GRCm39) probably benign Het
Mdn1 C T 4: 32,723,690 (GRCm39) P2542L probably damaging Het
Nadk A G 4: 155,668,711 (GRCm39) I127M probably benign Het
Nxph1 T A 6: 9,247,765 (GRCm39) Y245* probably null Het
Or4a73 C T 2: 89,421,046 (GRCm39) V138I probably benign Het
Or7s1a-ps1 T C 9: 18,843,990 (GRCm39) probably benign Het
Or8g34 G T 9: 39,373,563 (GRCm39) V276L probably benign Het
Or9k7 T A 10: 130,046,793 (GRCm39) T69S possibly damaging Het
Orc1 T C 4: 108,447,966 (GRCm39) F71S probably damaging Het
Pccb A T 9: 100,867,262 (GRCm39) Y404* probably null Het
Pde2a A C 7: 101,153,811 (GRCm39) I460L probably damaging Het
Ppp3cb G T 14: 20,578,263 (GRCm39) C162* probably null Het
Prickle2 T C 6: 92,353,511 (GRCm39) S652G probably benign Het
Prss38 A G 11: 59,266,309 (GRCm39) probably benign Het
Rcor3 T A 1: 191,821,813 (GRCm39) probably benign Het
Rgp1 C T 4: 43,579,440 (GRCm39) A16V probably damaging Het
Rptor G A 11: 119,734,539 (GRCm39) G514D probably damaging Het
Scnn1g T A 7: 121,365,489 (GRCm39) Y514N probably damaging Het
Sephs1 A G 2: 4,896,501 (GRCm39) D134G probably benign Het
Slc38a3 A G 9: 107,529,111 (GRCm39) probably benign Het
Slc6a1 A T 6: 114,287,182 (GRCm39) M388L probably benign Het
Ssbp3 A T 4: 106,904,655 (GRCm39) N350I probably damaging Het
Stam2 G A 2: 52,626,305 (GRCm39) probably benign Het
Sult1e1 A T 5: 87,726,445 (GRCm39) I223N probably damaging Het
Tcf20 C A 15: 82,740,582 (GRCm39) G290C probably damaging Het
Tekt2 G T 4: 126,216,057 (GRCm39) T412K possibly damaging Het
Trabd2b A G 4: 114,460,007 (GRCm39) T382A probably damaging Het
Ttn A T 2: 76,641,587 (GRCm39) L5176Q possibly damaging Het
Ubr4 C A 4: 139,204,543 (GRCm39) Y4818* probably null Het
Vmn1r204 A T 13: 22,741,069 (GRCm39) R233S probably damaging Het
Vmn1r86 A G 7: 12,836,382 (GRCm39) Y165H probably damaging Het
Yaf2 A C 15: 93,183,355 (GRCm39) C152G probably benign Het
Zfp804b A T 5: 6,820,703 (GRCm39) F751I probably benign Het
Other mutations in Ap3d1
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00094:Ap3d1 APN 10 80,577,813 (GRCm39) missense probably benign 0.00
IGL00827:Ap3d1 APN 10 80,549,393 (GRCm39) missense possibly damaging 0.92
IGL01668:Ap3d1 APN 10 80,554,993 (GRCm39) missense possibly damaging 0.95
IGL01934:Ap3d1 APN 10 80,545,092 (GRCm39) nonsense probably null
IGL03404:Ap3d1 APN 10 80,565,871 (GRCm39) missense probably damaging 1.00
christian UTSW 10 80,565,876 (GRCm39) missense probably damaging 1.00
Particle UTSW 10 80,546,328 (GRCm39) splice site probably null
vesicle UTSW 10 80,559,661 (GRCm39) missense probably damaging 1.00
R0119:Ap3d1 UTSW 10 80,559,449 (GRCm39) splice site probably benign
R0197:Ap3d1 UTSW 10 80,565,876 (GRCm39) missense probably damaging 1.00
R0356:Ap3d1 UTSW 10 80,563,812 (GRCm39) missense probably damaging 1.00
R0372:Ap3d1 UTSW 10 80,559,401 (GRCm39) missense probably damaging 1.00
R0491:Ap3d1 UTSW 10 80,555,075 (GRCm39) missense probably damaging 1.00
R0636:Ap3d1 UTSW 10 80,555,216 (GRCm39) nonsense probably null
R0792:Ap3d1 UTSW 10 80,544,313 (GRCm39) missense probably benign
R0942:Ap3d1 UTSW 10 80,568,789 (GRCm39) splice site probably benign
R1015:Ap3d1 UTSW 10 80,552,323 (GRCm39) missense probably damaging 1.00
R1023:Ap3d1 UTSW 10 80,550,092 (GRCm39) missense probably damaging 1.00
R1170:Ap3d1 UTSW 10 80,568,674 (GRCm39) splice site probably benign
R1540:Ap3d1 UTSW 10 80,551,775 (GRCm39) missense probably benign 0.00
R1639:Ap3d1 UTSW 10 80,565,844 (GRCm39) missense probably damaging 0.98
R1664:Ap3d1 UTSW 10 80,553,571 (GRCm39) nonsense probably null
R1669:Ap3d1 UTSW 10 80,546,670 (GRCm39) unclassified probably benign
R1839:Ap3d1 UTSW 10 80,562,942 (GRCm39) missense probably damaging 1.00
R1940:Ap3d1 UTSW 10 80,545,607 (GRCm39) missense probably benign 0.03
R2081:Ap3d1 UTSW 10 80,568,770 (GRCm39) missense probably damaging 1.00
R2258:Ap3d1 UTSW 10 80,556,966 (GRCm39) missense probably benign 0.03
R2281:Ap3d1 UTSW 10 80,549,832 (GRCm39) missense probably damaging 0.96
R2398:Ap3d1 UTSW 10 80,555,006 (GRCm39) nonsense probably null
R2849:Ap3d1 UTSW 10 80,577,742 (GRCm39) missense possibly damaging 0.65
R3856:Ap3d1 UTSW 10 80,548,019 (GRCm39) missense probably benign
R4350:Ap3d1 UTSW 10 80,555,119 (GRCm39) missense probably benign 0.15
R4590:Ap3d1 UTSW 10 80,555,646 (GRCm39) nonsense probably null
R4782:Ap3d1 UTSW 10 80,557,420 (GRCm39) splice site probably null
R4785:Ap3d1 UTSW 10 80,548,612 (GRCm39) frame shift probably null
R4834:Ap3d1 UTSW 10 80,555,560 (GRCm39) missense probably damaging 1.00
R4864:Ap3d1 UTSW 10 80,548,612 (GRCm39) frame shift probably null
R5051:Ap3d1 UTSW 10 80,555,033 (GRCm39) missense probably damaging 1.00
R5109:Ap3d1 UTSW 10 80,545,284 (GRCm39) missense probably benign 0.11
R5220:Ap3d1 UTSW 10 80,563,001 (GRCm39) missense probably damaging 1.00
R5307:Ap3d1 UTSW 10 80,559,383 (GRCm39) missense probably benign 0.29
R5586:Ap3d1 UTSW 10 80,554,964 (GRCm39) missense possibly damaging 0.92
R5796:Ap3d1 UTSW 10 80,549,871 (GRCm39) missense possibly damaging 0.70
R5905:Ap3d1 UTSW 10 80,558,761 (GRCm39) missense possibly damaging 0.50
R6025:Ap3d1 UTSW 10 80,546,298 (GRCm39) missense probably benign 0.01
R6028:Ap3d1 UTSW 10 80,558,761 (GRCm39) missense possibly damaging 0.50
R6364:Ap3d1 UTSW 10 80,546,328 (GRCm39) splice site probably null
R6469:Ap3d1 UTSW 10 80,547,992 (GRCm39) missense probably benign
R6603:Ap3d1 UTSW 10 80,549,881 (GRCm39) missense probably benign 0.04
R6872:Ap3d1 UTSW 10 80,550,156 (GRCm39) nonsense probably null
R6887:Ap3d1 UTSW 10 80,559,532 (GRCm39) missense probably damaging 1.00
R7249:Ap3d1 UTSW 10 80,577,767 (GRCm39) missense probably damaging 1.00
R7316:Ap3d1 UTSW 10 80,553,693 (GRCm39) missense probably damaging 1.00
R7325:Ap3d1 UTSW 10 80,559,637 (GRCm39) missense probably damaging 1.00
R7395:Ap3d1 UTSW 10 80,566,716 (GRCm39) missense probably benign 0.11
R7405:Ap3d1 UTSW 10 80,577,734 (GRCm39) missense probably benign 0.16
R7425:Ap3d1 UTSW 10 80,557,426 (GRCm39) missense probably damaging 1.00
R7558:Ap3d1 UTSW 10 80,558,755 (GRCm39) missense possibly damaging 0.92
R7583:Ap3d1 UTSW 10 80,545,292 (GRCm39) missense probably benign 0.13
R7703:Ap3d1 UTSW 10 80,553,678 (GRCm39) missense probably damaging 1.00
R7964:Ap3d1 UTSW 10 80,565,891 (GRCm39) missense probably damaging 1.00
R8021:Ap3d1 UTSW 10 80,550,135 (GRCm39) missense probably benign 0.30
R8200:Ap3d1 UTSW 10 80,558,766 (GRCm39) nonsense probably null
R8314:Ap3d1 UTSW 10 80,559,373 (GRCm39) missense possibly damaging 0.91
R8356:Ap3d1 UTSW 10 80,568,737 (GRCm39) missense probably damaging 1.00
R8896:Ap3d1 UTSW 10 80,552,425 (GRCm39) missense probably benign 0.01
R8936:Ap3d1 UTSW 10 80,547,952 (GRCm39) missense probably benign 0.02
R9183:Ap3d1 UTSW 10 80,545,627 (GRCm39) missense probably null 0.06
R9209:Ap3d1 UTSW 10 80,554,918 (GRCm39) missense probably benign 0.04
R9259:Ap3d1 UTSW 10 80,559,661 (GRCm39) missense probably damaging 1.00
R9476:Ap3d1 UTSW 10 80,545,655 (GRCm39) missense probably benign 0.00
R9645:Ap3d1 UTSW 10 80,545,062 (GRCm39) missense probably benign
R9664:Ap3d1 UTSW 10 80,548,639 (GRCm39) missense possibly damaging 0.71
R9781:Ap3d1 UTSW 10 80,545,609 (GRCm39) missense possibly damaging 0.51
X0019:Ap3d1 UTSW 10 80,554,936 (GRCm39) missense probably damaging 1.00
X0026:Ap3d1 UTSW 10 80,556,981 (GRCm39) missense possibly damaging 0.46
Z1088:Ap3d1 UTSW 10 80,555,071 (GRCm39) missense possibly damaging 0.91
Predicted Primers PCR Primer
(F):5'- ATGTGGCCCAAGAGTAGCAC -3'
(R):5'- GATCTTGGCAGTGAACTCCCTC -3'

Sequencing Primer
(F):5'- CAAGAGTAGCACCGAGACACG -3'
(R):5'- AGTGAACTCCCTCCCCTCAG -3'
Posted On 2016-07-22