Incidental Mutation 'R7963:Pdxdc1'
| ID |
650240 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Pdxdc1
|
| Ensembl Gene |
ENSMUSG00000022680 |
| Gene Name |
pyridoxal-dependent decarboxylase domain containing 1 |
| Synonyms |
2210010A19Rik |
| MMRRC Submission |
046006-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably non essential
(E-score: 0.192)
|
| Stock # |
R7963 (G1)
|
| Quality Score |
225.009 |
|
Status
|
Not validated
|
| Chromosome |
16 |
| Chromosomal Location |
13651012-13720995 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to T
at 13694030 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Tyrosine to Asparagine
at position 131
(Y131N)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000023361
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000023361]
[ENSMUST00000115802]
[ENSMUST00000115803]
[ENSMUST00000115804]
|
| AlphaFold |
no structure available at present |
| Predicted Effect |
possibly damaging
Transcript: ENSMUST00000023361
AA Change: Y131N
PolyPhen 2
Score 0.926 (Sensitivity: 0.81; Specificity: 0.94)
|
| SMART Domains |
Protein: ENSMUSP00000023361
Gene: ENSMUSG00000022680
AA Change: Y131N
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:Pyridoxal_deC
|
166 |
310 |
2.6e-12 |
PFAM |
|
coiled coil region
|
610 |
631 |
N/A |
INTRINSIC |
|
low complexity region
|
683 |
695 |
N/A |
INTRINSIC |
|
| Predicted Effect |
possibly damaging
Transcript: ENSMUST00000115802
AA Change: Y131N
PolyPhen 2
Score 0.956 (Sensitivity: 0.79; Specificity: 0.95)
|
| SMART Domains |
Protein: ENSMUSP00000111468
Gene: ENSMUSG00000022680
AA Change: Y131N
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:Pyridoxal_deC
|
153 |
316 |
1.8e-15 |
PFAM |
|
| Predicted Effect |
|
| SMART Domains |
Protein: ENSMUSP00000111469
Gene: ENSMUSG00000022680
AA Change: Y131N
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:Pyridoxal_deC
|
190 |
293 |
1.4e-13 |
PFAM |
|
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000115804
AA Change: Y131N
PolyPhen 2
Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)
|
| SMART Domains |
Protein: ENSMUSP00000111471
Gene: ENSMUSG00000022680
AA Change: Y131N
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:Pyridoxal_deC
|
154 |
308 |
5.5e-15 |
PFAM |
|
coiled coil region
|
610 |
631 |
N/A |
INTRINSIC |
|
low complexity region
|
683 |
695 |
N/A |
INTRINSIC |
|
| Coding Region Coverage |
- 1x: 100.0%
- 3x: 100.0%
- 10x: 99.7%
- 20x: 99.0%
|
| Validation Efficiency |
|
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 44 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 2210408I21Rik |
A |
G |
13: 77,340,673 (GRCm39) |
K101E |
probably benign |
Het |
| 4930407I10Rik |
A |
G |
15: 81,948,137 (GRCm39) |
K678R |
possibly damaging |
Het |
| Akr1b10 |
G |
C |
6: 34,364,643 (GRCm39) |
A35P |
possibly damaging |
Het |
| Arhgef10l |
T |
C |
4: 140,306,736 (GRCm39) |
E106G |
probably damaging |
Het |
| Atp9a |
T |
C |
2: 168,516,732 (GRCm39) |
Y445C |
probably damaging |
Het |
| Btbd18 |
T |
C |
2: 84,498,239 (GRCm39) |
S626P |
probably benign |
Het |
| Cdh23 |
A |
T |
10: 60,171,967 (GRCm39) |
N1738K |
probably damaging |
Het |
| Cdv3 |
T |
C |
9: 103,241,210 (GRCm39) |
D119G |
probably damaging |
Het |
| Cep295 |
A |
G |
9: 15,244,737 (GRCm39) |
F1240L |
possibly damaging |
Het |
| Cmtm1 |
CGGCACGTACTGAAGGTCGCTGACTGGATGGTGTGGCACGTACTGAAGGTCGCTGACTGGATGGTGTGGCACGTACTGAAGGTCGCTGACTGGATGGT |
CGGCACGTACTGAAGGTCGCTGACTGGATGGTGTGGCACGTACTGAAGGTCGCTGACTGGATGGT |
8: 105,036,102 (GRCm39) |
|
probably benign |
Het |
| Ctsr |
C |
A |
13: 61,310,276 (GRCm39) |
V127L |
probably damaging |
Het |
| Dlg1 |
G |
A |
16: 31,609,119 (GRCm39) |
R271Q |
probably null |
Het |
| Dnaaf11 |
A |
T |
15: 66,252,366 (GRCm39) |
D433E |
probably damaging |
Het |
| Dnajc1 |
G |
A |
2: 18,227,535 (GRCm39) |
T377I |
possibly damaging |
Het |
| F2rl3 |
T |
C |
8: 73,489,333 (GRCm39) |
Y187H |
probably damaging |
Het |
| Fgf1 |
A |
T |
18: 38,980,167 (GRCm39) |
V69E |
probably damaging |
Het |
| Garem1 |
T |
C |
18: 21,281,844 (GRCm39) |
K171E |
probably damaging |
Het |
| H3c13 |
C |
A |
3: 96,176,309 (GRCm39) |
Y100* |
probably null |
Het |
| Il2ra |
G |
A |
2: 11,679,235 (GRCm39) |
R65H |
probably benign |
Het |
| Lrp1b |
T |
C |
2: 40,817,947 (GRCm39) |
I2428V |
|
Het |
| Lrp3 |
G |
A |
7: 34,902,404 (GRCm39) |
Q579* |
probably null |
Het |
| Ncoa6 |
G |
A |
2: 155,247,916 (GRCm39) |
T1796I |
probably benign |
Het |
| Ncor1 |
T |
C |
11: 62,225,359 (GRCm39) |
I747V |
probably benign |
Het |
| Nfkb2 |
C |
T |
19: 46,298,358 (GRCm39) |
T554M |
possibly damaging |
Het |
| Nrde2 |
T |
C |
12: 100,116,127 (GRCm39) |
D119G |
probably damaging |
Het |
| Odf2 |
C |
A |
2: 29,816,112 (GRCm39) |
Q720K |
probably benign |
Het |
| Or4c52 |
T |
C |
2: 89,846,003 (GRCm39) |
V243A |
possibly damaging |
Het |
| Or4k41 |
T |
A |
2: 111,279,971 (GRCm39) |
L162Q |
possibly damaging |
Het |
| Or5w1b |
C |
T |
2: 87,475,769 (GRCm39) |
E233K |
probably benign |
Het |
| Or8k33 |
T |
C |
2: 86,383,639 (GRCm39) |
I276M |
possibly damaging |
Het |
| Pcx |
T |
C |
19: 4,652,034 (GRCm39) |
V94A |
probably damaging |
Het |
| Peg10 |
GC |
GCTCC |
6: 4,756,452 (GRCm39) |
|
probably benign |
Het |
| Plod2 |
A |
G |
9: 92,487,499 (GRCm39) |
H606R |
probably benign |
Het |
| Ptp4a2 |
A |
G |
4: 129,733,237 (GRCm39) |
|
probably benign |
Het |
| Rsl1 |
A |
G |
13: 67,330,173 (GRCm39) |
E207G |
probably damaging |
Het |
| Slc28a3 |
A |
G |
13: 58,724,580 (GRCm39) |
Y225H |
probably damaging |
Het |
| Spag17 |
T |
A |
3: 99,929,954 (GRCm39) |
M551K |
probably benign |
Het |
| Ssh2 |
C |
A |
11: 77,312,182 (GRCm39) |
A231D |
possibly damaging |
Het |
| Stab2 |
A |
G |
10: 86,683,887 (GRCm39) |
|
probably null |
Het |
| Stac2 |
T |
C |
11: 97,932,403 (GRCm39) |
T197A |
probably benign |
Het |
| Syne2 |
T |
A |
12: 76,067,174 (GRCm39) |
L4291Q |
probably benign |
Het |
| Vmn2r38 |
A |
T |
7: 9,095,854 (GRCm39) |
D179E |
probably benign |
Het |
| Zfp597 |
T |
C |
16: 3,689,022 (GRCm39) |
D51G |
probably benign |
Het |
| Zfp64 |
A |
T |
2: 168,793,538 (GRCm39) |
F69L |
probably benign |
Het |
|
| Other mutations in Pdxdc1 |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL01760:Pdxdc1
|
APN |
16 |
13,677,016 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL02101:Pdxdc1
|
APN |
16 |
13,687,720 (GRCm39) |
missense |
probably damaging |
0.99 |
|
IGL02484:Pdxdc1
|
APN |
16 |
13,693,945 (GRCm39) |
missense |
possibly damaging |
0.94 |
|
IGL02523:Pdxdc1
|
APN |
16 |
13,699,799 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL02560:Pdxdc1
|
APN |
16 |
13,657,596 (GRCm39) |
missense |
probably benign |
0.00 |
|
IGL02884:Pdxdc1
|
APN |
16 |
13,661,659 (GRCm39) |
missense |
possibly damaging |
0.86 |
|
IGL03008:Pdxdc1
|
APN |
16 |
13,694,023 (GRCm39) |
missense |
possibly damaging |
0.81 |
|
IGL03162:Pdxdc1
|
APN |
16 |
13,675,281 (GRCm39) |
missense |
probably damaging |
0.99 |
|
IGL02991:Pdxdc1
|
UTSW |
16 |
13,675,260 (GRCm39) |
missense |
probably damaging |
1.00 |
|
PIT4472001:Pdxdc1
|
UTSW |
16 |
13,663,209 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R0015:Pdxdc1
|
UTSW |
16 |
13,705,547 (GRCm39) |
splice site |
probably benign |
|
|
R0240:Pdxdc1
|
UTSW |
16 |
13,697,309 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R0240:Pdxdc1
|
UTSW |
16 |
13,697,309 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R0432:Pdxdc1
|
UTSW |
16 |
13,672,264 (GRCm39) |
missense |
probably damaging |
0.97 |
|
R0846:Pdxdc1
|
UTSW |
16 |
13,672,257 (GRCm39) |
critical splice donor site |
probably null |
|
|
R0944:Pdxdc1
|
UTSW |
16 |
13,656,233 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R0945:Pdxdc1
|
UTSW |
16 |
13,675,296 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1118:Pdxdc1
|
UTSW |
16 |
13,697,278 (GRCm39) |
splice site |
probably benign |
|
|
R1726:Pdxdc1
|
UTSW |
16 |
13,656,164 (GRCm39) |
critical splice donor site |
probably null |
|
|
R2425:Pdxdc1
|
UTSW |
16 |
13,697,372 (GRCm39) |
missense |
possibly damaging |
0.90 |
|
R3890:Pdxdc1
|
UTSW |
16 |
13,654,312 (GRCm39) |
missense |
probably benign |
|
|
R4452:Pdxdc1
|
UTSW |
16 |
13,654,990 (GRCm39) |
missense |
possibly damaging |
0.55 |
|
R4516:Pdxdc1
|
UTSW |
16 |
13,656,210 (GRCm39) |
nonsense |
probably null |
|
|
R4938:Pdxdc1
|
UTSW |
16 |
13,693,933 (GRCm39) |
missense |
probably benign |
0.03 |
|
R5352:Pdxdc1
|
UTSW |
16 |
13,658,175 (GRCm39) |
missense |
probably benign |
0.01 |
|
R5554:Pdxdc1
|
UTSW |
16 |
13,690,363 (GRCm39) |
missense |
probably benign |
0.01 |
|
R7300:Pdxdc1
|
UTSW |
16 |
13,697,374 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R7356:Pdxdc1
|
UTSW |
16 |
13,677,867 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8930:Pdxdc1
|
UTSW |
16 |
13,672,269 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8932:Pdxdc1
|
UTSW |
16 |
13,672,269 (GRCm39) |
missense |
probably damaging |
1.00 |
|
Z1176:Pdxdc1
|
UTSW |
16 |
13,720,907 (GRCm39) |
unclassified |
probably benign |
|
|
| Predicted Primers |
PCR Primer
(F):5'- ACCTGATTACAAAGGTATTGGCCC -3'
(R):5'- GAGGAACCTCCAGATTGATTTCC -3'
Sequencing Primer
(F):5'- CAGGCCAGGTCTAGCGG -3'
(R):5'- ACCTCCAGATTGATTTCCAGAGTGG -3'
|
| Posted On |
2020-09-15 |
Incidental Mutation