Incidental Mutation 'PIT4472001:Pdxdc1'
ID |
555886 |
Institutional Source |
Beutler Lab
|
Gene Symbol |
Pdxdc1
|
Ensembl Gene |
ENSMUSG00000022680 |
Gene Name |
pyridoxal-dependent decarboxylase domain containing 1 |
Synonyms |
2210010A19Rik |
Accession Numbers |
|
Essential gene? |
Probably non essential
(E-score: 0.173)
|
Stock # |
PIT4472001 (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 G
at 13663209 bp (GRCm39)
|
Zygosity |
Heterozygous |
Amino Acid Change |
Leucine to Proline
at position 428
(L428P)
|
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 |
probably damaging
Transcript: ENSMUST00000023361
AA Change: L428P
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
SMART Domains |
Protein: ENSMUSP00000023361 Gene: ENSMUSG00000022680 AA Change: L428P
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: ENSMUST00000115802
|
SMART Domains |
Protein: ENSMUSP00000111468 Gene: ENSMUSG00000022680
Domain | Start | End | E-Value | Type |
Pfam:Pyridoxal_deC
|
153 |
316 |
1.8e-15 |
PFAM |
|
Predicted Effect |
probably benign
Transcript: ENSMUST00000115803
|
SMART Domains |
Protein: ENSMUSP00000111469 Gene: ENSMUSG00000022680
Domain | Start | End | E-Value | Type |
Pfam:Pyridoxal_deC
|
190 |
293 |
1.4e-13 |
PFAM |
|
Predicted Effect |
probably damaging
Transcript: ENSMUST00000115804
AA Change: L428P
PolyPhen 2
Score 0.985 (Sensitivity: 0.74; Specificity: 0.96)
|
SMART Domains |
Protein: ENSMUSP00000111471 Gene: ENSMUSG00000022680 AA Change: L428P
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: 93.7%
- 3x: 90.8%
- 10x: 84.2%
- 20x: 70.1%
|
Validation Efficiency |
|
Allele List at MGI |
|
Other mutations in this stock |
Total: 47 list
Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
A4gnt |
C |
A |
9: 99,502,613 (GRCm39) |
P258T |
probably damaging |
Het |
Arvcf |
T |
C |
16: 18,221,699 (GRCm39) |
V714A |
possibly damaging |
Het |
Bcas3 |
A |
G |
11: 85,422,726 (GRCm39) |
I532V |
probably damaging |
Het |
Cbr1 |
T |
A |
16: 93,406,692 (GRCm39) |
V136E |
probably damaging |
Het |
Ccdc27 |
T |
C |
4: 154,126,184 (GRCm39) |
M102V |
unknown |
Het |
Ccr1 |
T |
C |
9: 123,763,765 (GRCm39) |
Y255C |
probably damaging |
Het |
Cd300e |
T |
A |
11: 114,945,336 (GRCm39) |
I153F |
possibly damaging |
Het |
Chd7 |
C |
T |
4: 8,753,101 (GRCm39) |
L533F |
unknown |
Het |
Cpvl |
A |
T |
6: 53,873,464 (GRCm39) |
F424Y |
possibly damaging |
Het |
Cxcl16 |
C |
T |
11: 70,349,625 (GRCm39) |
G80R |
probably damaging |
Het |
Cyp2g1 |
T |
C |
7: 26,513,619 (GRCm39) |
V186A |
probably benign |
Het |
Cyp4f15 |
T |
A |
17: 32,921,798 (GRCm39) |
M490K |
probably damaging |
Het |
D630045J12Rik |
A |
T |
6: 38,155,774 (GRCm39) |
V1160D |
probably damaging |
Het |
Dennd2b |
G |
A |
7: 109,130,337 (GRCm39) |
A888V |
probably damaging |
Het |
Fbn1 |
T |
C |
2: 125,148,421 (GRCm39) |
D2609G |
possibly damaging |
Het |
Fgf5 |
T |
A |
5: 98,409,838 (GRCm39) |
V129E |
probably damaging |
Het |
Fhl5 |
C |
A |
4: 25,211,194 (GRCm39) |
C166F |
probably damaging |
Het |
Frem1 |
G |
A |
4: 82,890,374 (GRCm39) |
T1035I |
probably benign |
Het |
Gcnt2 |
G |
A |
13: 41,071,413 (GRCm39) |
V19M |
probably benign |
Het |
Gga1 |
C |
A |
15: 78,777,836 (GRCm39) |
A595D |
probably damaging |
Het |
Gpaa1 |
C |
T |
15: 76,218,940 (GRCm39) |
T594I |
probably benign |
Het |
Gskip |
C |
T |
12: 105,651,121 (GRCm39) |
|
probably benign |
Het |
Ighv1-72 |
A |
G |
12: 115,721,620 (GRCm39) |
V112A |
probably damaging |
Het |
Krt16 |
T |
A |
11: 100,138,732 (GRCm39) |
T185S |
probably benign |
Het |
Lama1 |
T |
C |
17: 68,071,699 (GRCm39) |
V862A |
|
Het |
Lats2 |
A |
C |
14: 57,936,814 (GRCm39) |
Y558* |
probably null |
Het |
Mast4 |
G |
A |
13: 102,941,226 (GRCm39) |
T277M |
probably damaging |
Het |
Mnx1 |
T |
C |
5: 29,679,105 (GRCm39) |
E326G |
unknown |
Het |
Mtmr10 |
A |
G |
7: 63,983,106 (GRCm39) |
E471G |
probably benign |
Het |
Or5p64 |
C |
T |
7: 107,855,310 (GRCm39) |
V12M |
possibly damaging |
Het |
Otog |
G |
A |
7: 45,945,273 (GRCm39) |
V2177M |
probably damaging |
Het |
Ovgp1 |
A |
G |
3: 105,894,306 (GRCm39) |
E693G |
unknown |
Het |
Pclo |
T |
C |
5: 14,763,182 (GRCm39) |
M600T |
possibly damaging |
Het |
Pdgfra |
T |
A |
5: 75,340,907 (GRCm39) |
M622K |
probably damaging |
Het |
Pfkfb4 |
T |
C |
9: 108,828,222 (GRCm39) |
Y86H |
probably benign |
Het |
Pik3cg |
A |
G |
12: 32,254,983 (GRCm39) |
Y335H |
probably damaging |
Het |
Podnl1 |
G |
A |
8: 84,854,477 (GRCm39) |
V150M |
|
Het |
Pou4f3 |
A |
G |
18: 42,527,717 (GRCm39) |
M4V |
probably benign |
Het |
Ppp1r13b |
G |
A |
12: 111,799,074 (GRCm39) |
R864C |
probably damaging |
Het |
R3hdm4 |
A |
G |
10: 79,749,389 (GRCm39) |
|
probably null |
Het |
Skil |
T |
A |
3: 31,152,381 (GRCm39) |
V301D |
probably damaging |
Het |
Sptb |
G |
A |
12: 76,667,460 (GRCm39) |
T879M |
probably damaging |
Het |
Strip1 |
G |
A |
3: 107,535,486 (GRCm39) |
A79V |
probably benign |
Het |
Tpgs2 |
G |
A |
18: 25,301,652 (GRCm39) |
T5M |
possibly damaging |
Het |
Trim34a |
T |
A |
7: 103,897,155 (GRCm39) |
L73Q |
probably damaging |
Het |
Trpv4 |
T |
A |
5: 114,764,984 (GRCm39) |
T677S |
probably damaging |
Het |
Vmn2r23 |
A |
G |
6: 123,689,936 (GRCm39) |
T271A |
possibly 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 |
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 |
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'- AAAGTGAGTGGCTTGCCAG -3'
(R):5'- CATCAGAAAAGTATTAACAGGTCAGAC -3'
Sequencing Primer
(F):5'- CTTGCCAGAGGTAACAGTGTC -3'
(R):5'- GGGAGTGAATCCTTTCTGTG -3'
|
Posted On |
2019-06-07 |