Incidental Mutation 'R5109:Ap3d1'
| ID |
393752 |
| 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 |
042697-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably essential
(E-score: 0.931)
|
| Stock # |
R5109 (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 80545284 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Serine to Glycine
at position 1056
(S1056G)
|
| 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: S1056G
PolyPhen 2
Score 0.108 (Sensitivity: 0.93; Specificity: 0.86)
|
| SMART Domains |
Protein: ENSMUSP00000020420
Gene: ENSMUSG00000020198
AA Change: S1056G
| Domain | Start | End | E-Value | Type |
|---|
|
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
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:IZUMO
|
26 |
167 |
1.1e-31 |
PFAM |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000217823
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000218184
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000218330
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000218538
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000218610
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000219986
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000219987
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000219422
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000219816
|
| Meta Mutation Damage Score |
0.2800 |
| Coding Region Coverage |
- 1x: 99.1%
- 3x: 98.2%
- 10x: 95.9%
- 20x: 91.2%
|
| Validation Efficiency |
95% (78/82) |
| 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: 72 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Ankrd17 |
T |
C |
5: 90,391,395 (GRCm39) |
S1841G |
possibly damaging |
Het |
| Anxa10 |
T |
C |
8: 62,516,093 (GRCm39) |
E193G |
possibly damaging |
Het |
| Apbb1 |
T |
C |
7: 105,214,242 (GRCm39) |
N62D |
probably damaging |
Het |
| Apobec2 |
A |
T |
17: 48,730,022 (GRCm39) |
Y215N |
probably damaging |
Het |
| Apobec2 |
T |
A |
17: 48,730,024 (GRCm39) |
Y214F |
probably damaging |
Het |
| Appl2 |
A |
T |
10: 83,436,871 (GRCm39) |
V630E |
probably benign |
Het |
| Bud23 |
T |
C |
5: 135,089,877 (GRCm39) |
|
probably benign |
Het |
| Cacna1b |
A |
T |
2: 24,580,797 (GRCm39) |
M683K |
possibly damaging |
Het |
| Cbfa2t2 |
T |
A |
2: 154,373,293 (GRCm39) |
D187E |
probably damaging |
Het |
| Cfap54 |
G |
T |
10: 92,773,753 (GRCm39) |
F96L |
probably benign |
Het |
| Cimap1a |
A |
T |
7: 140,429,461 (GRCm39) |
S197C |
probably benign |
Het |
| Crebbp |
A |
G |
16: 3,906,295 (GRCm39) |
|
probably benign |
Het |
| Crocc |
C |
T |
4: 140,755,722 (GRCm39) |
R1102Q |
probably damaging |
Het |
| Dcaf12 |
T |
C |
4: 41,298,329 (GRCm39) |
D273G |
possibly damaging |
Het |
| Dchs1 |
T |
C |
7: 105,414,221 (GRCm39) |
T865A |
probably benign |
Het |
| Dhfr |
A |
T |
13: 92,491,788 (GRCm39) |
I8F |
probably damaging |
Het |
| Dnaja2 |
A |
T |
8: 86,279,887 (GRCm39) |
F97L |
possibly damaging |
Het |
| Dnase1l1 |
C |
T |
X: 73,320,644 (GRCm39) |
|
probably null |
Het |
| Doc2b |
T |
C |
11: 75,667,967 (GRCm39) |
D261G |
probably benign |
Het |
| Ear1 |
A |
G |
14: 44,056,485 (GRCm39) |
Y128H |
probably benign |
Het |
| Elac2 |
T |
A |
11: 64,883,142 (GRCm39) |
I171N |
probably damaging |
Het |
| Entpd3 |
C |
A |
9: 120,395,380 (GRCm39) |
N454K |
possibly damaging |
Het |
| Flrt3 |
A |
G |
2: 140,502,663 (GRCm39) |
S322P |
possibly damaging |
Het |
| Fn1 |
C |
T |
1: 71,688,394 (GRCm39) |
C170Y |
probably damaging |
Het |
| Gabbr1 |
T |
A |
17: 37,382,920 (GRCm39) |
|
probably benign |
Het |
| Gm7247 |
T |
G |
14: 51,602,774 (GRCm39) |
S37A |
probably damaging |
Het |
| Gm8775 |
T |
A |
3: 4,277,008 (GRCm39) |
|
noncoding transcript |
Het |
| Gprc5c |
G |
T |
11: 114,755,093 (GRCm39) |
V257L |
possibly damaging |
Het |
| Gria4 |
A |
C |
9: 4,472,168 (GRCm39) |
N440K |
probably damaging |
Het |
| H2-T22 |
T |
A |
17: 36,350,113 (GRCm39) |
R334* |
probably null |
Het |
| Ift172 |
T |
C |
5: 31,423,330 (GRCm39) |
D817G |
probably benign |
Het |
| Igkv9-124 |
T |
A |
6: 67,919,348 (GRCm39) |
R21S |
possibly damaging |
Het |
| Itgam |
G |
A |
7: 127,712,390 (GRCm39) |
V846I |
probably benign |
Het |
| Kif11 |
T |
A |
19: 37,373,063 (GRCm39) |
M94K |
possibly damaging |
Het |
| Krtcap2 |
T |
C |
3: 89,154,085 (GRCm39) |
V2A |
probably benign |
Het |
| Lrrc47 |
A |
G |
4: 154,101,933 (GRCm39) |
D400G |
probably damaging |
Het |
| Man2a1 |
T |
A |
17: 65,059,443 (GRCm39) |
V1110E |
probably benign |
Het |
| Mfsd9 |
T |
A |
1: 40,813,365 (GRCm39) |
I317F |
probably damaging |
Het |
| Mindy4 |
A |
T |
6: 55,193,730 (GRCm39) |
|
probably null |
Het |
| Mrpl53 |
A |
G |
6: 83,086,541 (GRCm39) |
T82A |
probably damaging |
Het |
| Myo3b |
A |
G |
2: 69,925,637 (GRCm39) |
K35E |
possibly damaging |
Het |
| Nalcn |
A |
G |
14: 123,515,650 (GRCm39) |
V1717A |
possibly damaging |
Het |
| Ncoa2 |
A |
G |
1: 13,257,070 (GRCm39) |
V143A |
probably damaging |
Het |
| Ndufa9 |
A |
C |
6: 126,809,520 (GRCm39) |
|
probably null |
Het |
| Or10ag60 |
G |
A |
2: 87,438,319 (GRCm39) |
G196R |
possibly damaging |
Het |
| Or10ag60 |
G |
A |
2: 87,437,755 (GRCm39) |
A8T |
possibly damaging |
Het |
| Or12e9 |
A |
G |
2: 87,201,878 (GRCm39) |
M1V |
probably null |
Het |
| Or5k17 |
A |
G |
16: 58,746,422 (GRCm39) |
S171P |
probably benign |
Het |
| Or5p55 |
T |
C |
7: 107,567,104 (GRCm39) |
S167P |
probably benign |
Het |
| Or6c202 |
T |
C |
10: 128,996,106 (GRCm39) |
Y249C |
probably damaging |
Het |
| Or7g28 |
A |
T |
9: 19,272,438 (GRCm39) |
I71N |
probably damaging |
Het |
| Or9g8 |
G |
A |
2: 85,607,668 (GRCm39) |
V247M |
probably damaging |
Het |
| Pde4b |
G |
T |
4: 102,458,741 (GRCm39) |
A466S |
probably damaging |
Het |
| Pfkfb3 |
A |
T |
2: 11,491,162 (GRCm39) |
|
probably benign |
Het |
| Ppp1r21 |
A |
G |
17: 88,866,268 (GRCm39) |
K355E |
probably damaging |
Het |
| Psme4 |
T |
A |
11: 30,741,095 (GRCm39) |
Y90* |
probably null |
Het |
| Rbms1 |
G |
A |
2: 60,612,284 (GRCm39) |
L161F |
probably damaging |
Het |
| Rdh16f2 |
A |
G |
10: 127,702,672 (GRCm39) |
D83G |
probably damaging |
Het |
| Sec16b |
C |
T |
1: 157,392,361 (GRCm39) |
R910* |
probably null |
Het |
| Sema4c |
CTGGGCTT |
C |
1: 36,591,381 (GRCm39) |
|
probably null |
Het |
| Spata31e5 |
T |
C |
1: 28,816,636 (GRCm39) |
I465M |
possibly damaging |
Het |
| Stambp |
A |
G |
6: 83,540,803 (GRCm39) |
|
probably null |
Het |
| Tcf21 |
T |
C |
10: 22,695,558 (GRCm39) |
N82S |
probably damaging |
Het |
| Tlr2 |
A |
T |
3: 83,745,030 (GRCm39) |
V351D |
probably damaging |
Het |
| Tmem39a |
G |
A |
16: 38,411,326 (GRCm39) |
G359D |
probably damaging |
Het |
| Ttc23l |
G |
T |
15: 10,551,636 (GRCm39) |
T30K |
possibly damaging |
Het |
| Vmn2r17 |
C |
A |
5: 109,577,342 (GRCm39) |
F464L |
probably benign |
Het |
| Vmn2r49 |
T |
A |
7: 9,710,204 (GRCm39) |
T843S |
probably benign |
Het |
| Vmn2r7 |
T |
C |
3: 64,598,088 (GRCm39) |
D823G |
probably null |
Het |
| Wrnip1 |
T |
A |
13: 33,000,319 (GRCm39) |
L442Q |
probably damaging |
Het |
| Zbtb38 |
G |
T |
9: 96,569,062 (GRCm39) |
S674Y |
probably damaging |
Het |
| Zfp639 |
T |
G |
3: 32,574,585 (GRCm39) |
|
probably null |
Het |
|
| Other mutations in Ap3d1 |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH 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 |
|
R5219:Ap3d1
|
UTSW |
10 |
80,545,651 (GRCm39) |
missense |
probably benign |
0.03 |
|
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'- AACTTCTCATGGGTGGCTC -3'
(R):5'- AAGCTCTTGATGACCCTCCC -3'
Sequencing Primer
(F):5'- ATGGGTGGCTCCTTCATCATC -3'
(R):5'- GTGCTACTCTTGGGCCACATG -3'
|
| Posted On |
2016-06-15 |
Incidental Mutation