Incidental Mutation 'R4516:Pdxdc1'
| ID |
332931 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Pdxdc1
|
| Ensembl Gene |
ENSMUSG00000022680 |
| Gene Name |
pyridoxal-dependent decarboxylase domain containing 1 |
| Synonyms |
2210010A19Rik |
| MMRRC Submission |
041760-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably non essential
(E-score: 0.173)
|
| Stock # |
R4516 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
16 |
| Chromosomal Location |
13651012-13720995 bp(-) (GRCm39) |
| Type of Mutation |
nonsense |
| DNA Base Change (assembly) |
G to A
at 13656210 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Glutamine to Stop codon
at position 621
(Q621*)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000111471
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000023361]
[ENSMUST00000023362]
[ENSMUST00000115804]
[ENSMUST00000115805]
|
| AlphaFold |
no structure available at present |
| Predicted Effect |
probably null
Transcript: ENSMUST00000023361
AA Change: Q621*
|
| SMART Domains |
Protein: ENSMUSP00000023361
Gene: ENSMUSG00000022680
AA Change: Q621*
| 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 null
Transcript: ENSMUST00000115804
AA Change: Q621*
|
| SMART Domains |
Protein: ENSMUSP00000111471
Gene: ENSMUSG00000022680
AA Change: Q621*
| 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: ENSMUST00000124860
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000127432
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000136618
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000148848
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000154150
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000139161
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000150435
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000144913
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000152450
|
| Meta Mutation Damage Score |
0.9755 |
| Coding Region Coverage |
- 1x: 99.4%
- 3x: 98.5%
- 10x: 96.6%
- 20x: 92.9%
|
| Validation Efficiency |
86% (51/59) |
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 47 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Bean1 |
T |
C |
8: 104,941,786 (GRCm39) |
S211P |
probably damaging |
Het |
| Bltp1 |
T |
C |
3: 36,949,460 (GRCm39) |
S369P |
possibly damaging |
Het |
| Camta1 |
A |
G |
4: 151,229,177 (GRCm39) |
S552P |
possibly damaging |
Het |
| Cdh11 |
T |
C |
8: 103,400,594 (GRCm39) |
T125A |
possibly damaging |
Het |
| Cdk5rap2 |
A |
T |
4: 70,194,952 (GRCm39) |
|
probably null |
Het |
| Cenpc1 |
A |
G |
5: 86,195,446 (GRCm39) |
S108P |
possibly damaging |
Het |
| Cfap20dc |
A |
T |
14: 8,536,609 (GRCm38) |
D199E |
probably damaging |
Het |
| Cfap44 |
T |
A |
16: 44,294,227 (GRCm39) |
Y224* |
probably null |
Het |
| Cfap46 |
G |
A |
7: 139,239,998 (GRCm39) |
|
probably benign |
Het |
| Cntrl |
G |
A |
2: 35,017,993 (GRCm39) |
V468I |
probably benign |
Het |
| Col6a6 |
C |
T |
9: 105,576,148 (GRCm39) |
V2071I |
possibly damaging |
Het |
| Coq7 |
A |
T |
7: 118,109,130 (GRCm39) |
L306Q |
unknown |
Het |
| D7Ertd443e |
C |
G |
7: 133,895,057 (GRCm39) |
Q591H |
probably damaging |
Het |
| Dchs1 |
C |
T |
7: 105,404,059 (GRCm39) |
V2828M |
probably damaging |
Het |
| Dzank1 |
T |
A |
2: 144,352,042 (GRCm39) |
|
probably benign |
Het |
| Elmo1 |
C |
T |
13: 20,467,084 (GRCm39) |
T235I |
probably benign |
Het |
| Elp3 |
A |
T |
14: 65,785,326 (GRCm39) |
F492I |
possibly damaging |
Het |
| Espl1 |
A |
G |
15: 102,231,671 (GRCm39) |
S90G |
probably benign |
Het |
| Fbxl20 |
T |
C |
11: 97,986,061 (GRCm39) |
|
probably benign |
Het |
| Gm10722 |
T |
C |
9: 3,000,937 (GRCm39) |
C6R |
probably benign |
Het |
| Got1 |
T |
C |
19: 43,493,280 (GRCm39) |
Y243C |
probably damaging |
Het |
| Hipk1 |
G |
T |
3: 103,657,688 (GRCm39) |
H799N |
probably damaging |
Het |
| Kif21a |
A |
T |
15: 90,855,345 (GRCm39) |
M673K |
probably benign |
Het |
| Lama3 |
T |
A |
18: 12,628,415 (GRCm39) |
D1502E |
probably damaging |
Het |
| Limk1 |
A |
G |
5: 134,705,640 (GRCm39) |
|
probably benign |
Het |
| Myo5b |
A |
G |
18: 74,758,745 (GRCm39) |
Y242C |
probably damaging |
Het |
| Naa12 |
G |
A |
18: 80,254,791 (GRCm39) |
M28I |
probably benign |
Het |
| Ncbp1 |
T |
C |
4: 46,157,824 (GRCm39) |
V354A |
probably damaging |
Het |
| Ncoa2 |
T |
C |
1: 13,217,130 (GRCm39) |
D1380G |
probably damaging |
Het |
| Ntng1 |
A |
G |
3: 109,842,329 (GRCm39) |
I148T |
probably damaging |
Het |
| Oas1d |
A |
T |
5: 121,057,233 (GRCm39) |
T280S |
probably damaging |
Het |
| Or1e29 |
C |
T |
11: 73,667,866 (GRCm39) |
G96S |
probably benign |
Het |
| Or4c15b |
T |
A |
2: 89,113,187 (GRCm39) |
M118L |
probably benign |
Het |
| Pax7 |
T |
G |
4: 139,508,104 (GRCm39) |
D307A |
probably benign |
Het |
| Rab29 |
A |
T |
1: 131,795,469 (GRCm39) |
Y27F |
possibly damaging |
Het |
| Rab3gap2 |
G |
A |
1: 184,999,265 (GRCm39) |
V991I |
probably benign |
Het |
| Ric1 |
A |
G |
19: 29,548,165 (GRCm39) |
T278A |
probably benign |
Het |
| Rufy4 |
T |
C |
1: 74,186,822 (GRCm39) |
C537R |
probably damaging |
Het |
| Slc47a1 |
T |
C |
11: 61,235,339 (GRCm39) |
H498R |
probably benign |
Het |
| Spmip6 |
T |
C |
4: 41,517,200 (GRCm39) |
|
probably benign |
Het |
| Tas2r116 |
T |
C |
6: 132,833,113 (GRCm39) |
L238P |
probably damaging |
Het |
| Tigd5 |
A |
T |
15: 75,782,364 (GRCm39) |
R252* |
probably null |
Het |
| Tlr6 |
A |
G |
5: 65,112,247 (GRCm39) |
F220S |
possibly damaging |
Het |
| Tmem106b |
C |
T |
6: 13,075,098 (GRCm39) |
T95I |
probably damaging |
Het |
| Ubqlnl |
C |
T |
7: 103,798,925 (GRCm39) |
V191M |
probably benign |
Het |
| Vmn1r174 |
A |
G |
7: 23,453,768 (GRCm39) |
I145V |
probably benign |
Het |
| Vps26a |
T |
C |
10: 62,304,124 (GRCm39) |
M116V |
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 |
|
R3890:Pdxdc1
|
UTSW |
16 |
13,654,312 (GRCm39) |
missense |
probably benign |
|
|
R4452:Pdxdc1
|
UTSW |
16 |
13,654,990 (GRCm39) |
missense |
possibly damaging |
0.55 |
|
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'- AGCCTGGACTGGAGAAAACC -3'
(R):5'- CTGCTCATGTACTTCAGTGCAG -3'
Sequencing Primer
(F):5'- CACGGATCCTACTACAGGGATTTG -3'
(R):5'- GCTCATGTACTTCAGTGCAGAATTC -3'
|
| Posted On |
2015-08-18 |
Incidental Mutation