Incidental Mutation 'R3890:Pdxdc1'
ID |
310366 |
Institutional Source |
Beutler Lab
|
Gene Symbol |
Pdxdc1
|
Ensembl Gene |
ENSMUSG00000022680 |
Gene Name |
pyridoxal-dependent decarboxylase domain containing 1 |
Synonyms |
2210010A19Rik |
MMRRC Submission |
040802-MU
|
Accession Numbers |
|
Essential gene? |
Probably non essential
(E-score: 0.173)
|
Stock # |
R3890 (G1)
|
Quality Score |
225 |
Status
|
Validated
|
Chromosome |
16 |
Chromosomal Location |
13651012-13720995 bp(-) (GRCm39) |
Type of Mutation |
missense |
DNA Base Change (assembly) |
T to C
at 13654312 bp (GRCm39)
|
Zygosity |
Heterozygous |
Amino Acid Change |
Threonine to Alanine
at position 759
(T759A)
|
Ref Sequence |
ENSEMBL: ENSMUSP00000023361
(fasta)
|
Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000023361]
[ENSMUST00000023362]
[ENSMUST00000115804]
[ENSMUST00000115805]
|
AlphaFold |
no structure available at present |
Predicted Effect |
probably benign
Transcript: ENSMUST00000023361
AA Change: T759A
PolyPhen 2
Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
|
SMART Domains |
Protein: ENSMUSP00000023361 Gene: ENSMUSG00000022680 AA Change: T759A
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 |
probably benign
Transcript: ENSMUST00000023362
|
SMART Domains |
Protein: ENSMUSP00000023362 Gene: ENSMUSG00000022681
Domain | Start | End | E-Value | Type |
Pfam:N_Asn_amidohyd
|
36 |
304 |
1.3e-124 |
PFAM |
|
Predicted Effect |
probably benign
Transcript: ENSMUST00000115804
|
SMART Domains |
Protein: ENSMUSP00000111471 Gene: ENSMUSG00000022680
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 |
|
Predicted Effect |
probably benign
Transcript: ENSMUST00000115805
|
SMART Domains |
Protein: ENSMUSP00000111472 Gene: ENSMUSG00000022681
Domain | Start | End | E-Value | Type |
Pfam:N_Asn_amidohyd
|
32 |
215 |
1.4e-82 |
PFAM |
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000123849
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000124604
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000124860
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000152450
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000127432
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000145248
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000150435
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000139161
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000144913
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000148848
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000154150
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000136618
|
Meta Mutation Damage Score |
0.0898 |
Coding Region Coverage |
- 1x: 99.2%
- 3x: 98.6%
- 10x: 97.2%
- 20x: 94.9%
|
Validation Efficiency |
98% (60/61) |
Allele List at MGI |
|
Other mutations in this stock |
Total: 59 list
Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
1700029H14Rik |
T |
C |
8: 13,604,700 (GRCm39) |
Y201C |
probably damaging |
Het |
Adam10 |
A |
G |
9: 70,676,136 (GRCm39) |
T624A |
probably benign |
Het |
Atf2 |
T |
C |
2: 73,693,557 (GRCm39) |
S2G |
probably damaging |
Het |
Atf7ip |
T |
C |
6: 136,564,043 (GRCm39) |
V762A |
possibly damaging |
Het |
Cacna1e |
C |
T |
1: 154,359,299 (GRCm39) |
R265Q |
probably damaging |
Het |
Cckbr |
A |
C |
7: 105,075,376 (GRCm39) |
T49P |
probably benign |
Het |
Clip2 |
T |
C |
5: 134,551,847 (GRCm39) |
K92E |
probably damaging |
Het |
Clrn3 |
T |
C |
7: 135,120,194 (GRCm39) |
T131A |
possibly damaging |
Het |
Cntrl |
T |
G |
2: 35,060,492 (GRCm39) |
C1342G |
probably benign |
Het |
Def8 |
T |
C |
8: 124,185,083 (GRCm39) |
|
probably benign |
Het |
Dennd4a |
T |
C |
9: 64,779,310 (GRCm39) |
S598P |
probably damaging |
Het |
Deup1 |
A |
G |
9: 15,511,009 (GRCm39) |
Y257H |
probably damaging |
Het |
Dnajc28 |
G |
A |
16: 91,413,755 (GRCm39) |
T187M |
probably damaging |
Het |
Ect2 |
T |
C |
3: 27,192,689 (GRCm39) |
D387G |
probably damaging |
Het |
Fat3 |
G |
A |
9: 15,909,567 (GRCm39) |
S2145F |
probably damaging |
Het |
Fmo4 |
A |
T |
1: 162,621,624 (GRCm39) |
I529N |
probably benign |
Het |
Frs3 |
A |
G |
17: 48,014,360 (GRCm39) |
D351G |
probably damaging |
Het |
Gcat |
T |
A |
15: 78,921,376 (GRCm39) |
V378D |
probably damaging |
Het |
Hmcn1 |
A |
T |
1: 150,510,946 (GRCm39) |
D3592E |
probably damaging |
Het |
Hspa4l |
A |
T |
3: 40,736,026 (GRCm39) |
Q570L |
possibly damaging |
Het |
Ifi213 |
A |
G |
1: 173,394,822 (GRCm39) |
I571T |
probably benign |
Het |
Lsamp |
T |
C |
16: 39,805,054 (GRCm39) |
V11A |
probably benign |
Het |
Mettl1 |
T |
C |
10: 126,880,998 (GRCm39) |
|
probably null |
Het |
Mettl15 |
A |
G |
2: 109,021,924 (GRCm39) |
I127T |
probably benign |
Het |
Mipep |
T |
C |
14: 61,046,444 (GRCm39) |
L322P |
probably damaging |
Het |
Mob1b |
T |
A |
5: 88,901,061 (GRCm39) |
I156K |
probably damaging |
Het |
Mobp |
G |
A |
9: 119,997,022 (GRCm39) |
C51Y |
probably damaging |
Het |
Ms4a3 |
T |
C |
19: 11,610,271 (GRCm39) |
N97S |
probably benign |
Het |
Myrip |
A |
G |
9: 120,251,324 (GRCm39) |
E210G |
probably damaging |
Het |
Nos1ap |
T |
C |
1: 170,177,025 (GRCm39) |
Y126C |
probably damaging |
Het |
Nuak2 |
G |
T |
1: 132,259,223 (GRCm39) |
A342S |
possibly damaging |
Het |
Obscn |
T |
C |
11: 59,022,472 (GRCm39) |
R758G |
possibly damaging |
Het |
Or10ah1-ps1 |
G |
T |
5: 143,123,152 (GRCm39) |
S290R |
probably benign |
Het |
Or2aj5 |
A |
G |
16: 19,425,205 (GRCm39) |
I71T |
probably damaging |
Het |
Or7e165 |
T |
G |
9: 19,695,011 (GRCm39) |
I194S |
probably benign |
Het |
Pdgfra |
A |
G |
5: 75,328,588 (GRCm39) |
N240S |
probably null |
Het |
Pex2 |
C |
T |
3: 5,626,008 (GRCm39) |
C267Y |
probably damaging |
Het |
Pgghg |
T |
C |
7: 140,525,616 (GRCm39) |
I473T |
probably damaging |
Het |
Prdm15 |
T |
C |
16: 97,600,771 (GRCm39) |
H829R |
probably damaging |
Het |
Pum1 |
T |
C |
4: 130,491,393 (GRCm39) |
L774P |
probably damaging |
Het |
Rcbtb1 |
T |
A |
14: 59,465,804 (GRCm39) |
H382Q |
possibly damaging |
Het |
Rprd2 |
A |
T |
3: 95,672,536 (GRCm39) |
F956I |
probably damaging |
Het |
Samd1 |
G |
A |
8: 84,724,361 (GRCm39) |
|
probably benign |
Het |
Slc4a11 |
A |
T |
2: 130,527,705 (GRCm39) |
S592T |
probably damaging |
Het |
Slc5a4b |
A |
G |
10: 75,898,094 (GRCm39) |
V540A |
probably benign |
Het |
Slfn8 |
G |
A |
11: 82,895,270 (GRCm39) |
T512I |
possibly damaging |
Het |
Slx4 |
A |
T |
16: 3,797,773 (GRCm39) |
I1537N |
probably damaging |
Het |
Sorl1 |
G |
A |
9: 41,915,401 (GRCm39) |
T1276M |
probably damaging |
Het |
Specc1 |
C |
T |
11: 62,042,739 (GRCm39) |
T872M |
probably benign |
Het |
Speer4f1 |
T |
C |
5: 17,684,500 (GRCm39) |
I176T |
probably damaging |
Het |
Spint1 |
T |
C |
2: 119,079,283 (GRCm39) |
I455T |
probably benign |
Het |
Srp54a |
A |
G |
12: 55,135,978 (GRCm39) |
|
probably null |
Het |
Stoml3 |
T |
A |
3: 53,414,875 (GRCm39) |
N222K |
probably damaging |
Het |
Syce1 |
C |
A |
7: 140,359,809 (GRCm39) |
L83F |
probably damaging |
Het |
Tanc2 |
A |
T |
11: 105,689,504 (GRCm39) |
D222V |
probably damaging |
Het |
Tasor2 |
T |
C |
13: 3,646,785 (GRCm39) |
E80G |
probably damaging |
Het |
Thsd7a |
G |
A |
6: 12,418,336 (GRCm39) |
S631L |
probably benign |
Het |
Vmn2r73 |
G |
A |
7: 85,507,144 (GRCm39) |
H723Y |
probably benign |
Het |
Wdfy4 |
T |
C |
14: 32,769,237 (GRCm39) |
E2076G |
probably damaging |
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 |
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 |
R7963:Pdxdc1
|
UTSW |
16 |
13,694,030 (GRCm39) |
missense |
possibly damaging |
0.93 |
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'- TGGCATAGTTCACGTCTTCC -3'
(R):5'- TCAGGACCACAGAGCCTTTG -3'
Sequencing Primer
(F):5'- GGCATAGTTCACGTCTTCCATAGAAC -3'
(R):5'- GTCTCATGTCCCTAGGTCAGAAG -3'
|
Posted On |
2015-04-17 |