Incidental Mutation 'R5352:Pdxdc1'
ID |
423867 |
Institutional Source |
Beutler Lab
|
Gene Symbol |
Pdxdc1
|
Ensembl Gene |
ENSMUSG00000022680 |
Gene Name |
pyridoxal-dependent decarboxylase domain containing 1 |
Synonyms |
2210010A19Rik |
MMRRC Submission |
042931-MU
|
Accession Numbers |
|
Essential gene? |
Probably non essential
(E-score: 0.173)
|
Stock # |
R5352 (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 13658175 bp (GRCm39)
|
Zygosity |
Heterozygous |
Amino Acid Change |
Asparagine to Serine
at position 516
(N516S)
|
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: N516S
PolyPhen 2
Score 0.010 (Sensitivity: 0.96; Specificity: 0.77)
|
SMART Domains |
Protein: ENSMUSP00000023361 Gene: ENSMUSG00000022680 AA Change: N516S
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
AA Change: N516S
PolyPhen 2
Score 0.009 (Sensitivity: 0.96; Specificity: 0.77)
|
SMART Domains |
Protein: ENSMUSP00000111471 Gene: ENSMUSG00000022680 AA Change: N516S
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: ENSMUST00000144913
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000150435
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000154150
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000152450
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000148848
|
Meta Mutation Damage Score |
0.0604 |
Coding Region Coverage |
- 1x: 99.3%
- 3x: 98.7%
- 10x: 97.5%
- 20x: 95.9%
|
Validation Efficiency |
100% (66/66) |
Allele List at MGI |
|
Other mutations in this stock |
Total: 57 list
Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
A630010A05Rik |
T |
G |
16: 14,436,565 (GRCm39) |
L206* |
probably null |
Het |
Adgrv1 |
T |
C |
13: 81,642,776 (GRCm39) |
Y3218C |
probably damaging |
Het |
Agtpbp1 |
G |
A |
13: 59,621,560 (GRCm39) |
T41M |
probably damaging |
Het |
Akap6 |
A |
T |
12: 52,842,880 (GRCm39) |
E76V |
probably damaging |
Het |
Ank2 |
C |
A |
3: 127,292,640 (GRCm39) |
|
probably benign |
Het |
Atp6ap1l |
A |
C |
13: 91,031,875 (GRCm39) |
L269R |
probably damaging |
Het |
Blk |
A |
G |
14: 63,613,420 (GRCm39) |
S363P |
probably damaging |
Het |
Bltp3a |
G |
A |
17: 28,106,489 (GRCm39) |
S1005N |
probably benign |
Het |
Btnl9 |
T |
C |
11: 49,069,667 (GRCm39) |
N204S |
probably benign |
Het |
Cc2d2a |
G |
T |
5: 43,863,555 (GRCm39) |
W672C |
probably damaging |
Het |
Ccnf |
A |
G |
17: 24,462,247 (GRCm39) |
|
probably null |
Het |
Cdc45 |
C |
T |
16: 18,614,647 (GRCm39) |
R205H |
probably damaging |
Het |
Chst1 |
A |
G |
2: 92,443,710 (GRCm39) |
T61A |
possibly damaging |
Het |
Col6a4 |
G |
A |
9: 105,938,743 (GRCm39) |
T1325I |
probably damaging |
Het |
Col7a1 |
A |
C |
9: 108,790,479 (GRCm39) |
T976P |
unknown |
Het |
Corin |
C |
T |
5: 72,462,376 (GRCm39) |
S811N |
probably benign |
Het |
Dnal1 |
T |
C |
12: 84,183,322 (GRCm39) |
V27A |
possibly damaging |
Het |
Dusp29 |
G |
A |
14: 21,727,091 (GRCm39) |
R186W |
probably benign |
Het |
F830045P16Rik |
T |
A |
2: 129,314,821 (GRCm39) |
H152L |
probably damaging |
Het |
Flnc |
A |
G |
6: 29,449,317 (GRCm39) |
S1405G |
possibly damaging |
Het |
Foxj1 |
T |
C |
11: 116,224,905 (GRCm39) |
N154S |
possibly damaging |
Het |
Gm12183 |
T |
C |
11: 48,642,989 (GRCm39) |
|
noncoding transcript |
Het |
Gm27047 |
G |
A |
6: 130,607,982 (GRCm39) |
|
noncoding transcript |
Het |
Grm5 |
A |
G |
7: 87,724,058 (GRCm39) |
I783V |
probably damaging |
Het |
Hk1 |
A |
T |
10: 62,140,549 (GRCm39) |
S113T |
probably damaging |
Het |
Iqca1 |
A |
T |
1: 90,057,918 (GRCm39) |
N260K |
probably benign |
Het |
Iws1 |
A |
T |
18: 32,216,457 (GRCm39) |
K399M |
probably damaging |
Het |
Kdm4d |
A |
G |
9: 14,375,654 (GRCm39) |
I68T |
probably damaging |
Het |
Man2a1 |
T |
C |
17: 65,038,241 (GRCm39) |
I75T |
probably damaging |
Het |
Med13 |
T |
A |
11: 86,192,294 (GRCm39) |
I824L |
possibly damaging |
Het |
Meioc |
A |
T |
11: 102,566,139 (GRCm39) |
E585V |
probably benign |
Het |
Mrgpre |
A |
C |
7: 143,334,831 (GRCm39) |
F224C |
probably damaging |
Het |
Muc5b |
T |
A |
7: 141,418,295 (GRCm39) |
F3747Y |
possibly damaging |
Het |
Nherf2 |
C |
T |
17: 24,861,229 (GRCm39) |
R66H |
probably damaging |
Het |
Nlrp4e |
T |
C |
7: 23,052,598 (GRCm39) |
V839A |
probably benign |
Het |
Nup210 |
A |
T |
6: 91,046,298 (GRCm39) |
V545E |
probably damaging |
Het |
Ola1 |
T |
C |
2: 72,929,674 (GRCm39) |
T310A |
probably damaging |
Het |
Phlpp1 |
A |
G |
1: 106,100,455 (GRCm39) |
D241G |
probably benign |
Het |
Ppp1r36 |
T |
C |
12: 76,474,857 (GRCm39) |
V85A |
probably damaging |
Het |
Rasa3 |
A |
C |
8: 13,681,778 (GRCm39) |
L57R |
possibly damaging |
Het |
Rp1 |
T |
C |
1: 4,417,321 (GRCm39) |
S1264G |
probably benign |
Het |
Rprd1b |
A |
G |
2: 157,900,656 (GRCm39) |
E247G |
probably damaging |
Het |
Sag |
G |
T |
1: 87,740,715 (GRCm39) |
V46L |
probably benign |
Het |
Sat2 |
A |
T |
11: 69,513,141 (GRCm39) |
I17F |
probably damaging |
Het |
Slc39a6 |
A |
T |
18: 24,734,093 (GRCm39) |
Y199N |
probably benign |
Het |
Snx2 |
A |
G |
18: 53,330,997 (GRCm39) |
|
probably null |
Het |
Thbs4 |
T |
C |
13: 92,900,098 (GRCm39) |
D466G |
probably damaging |
Het |
Tmem208 |
A |
G |
8: 106,055,063 (GRCm39) |
D91G |
probably damaging |
Het |
Tmf1 |
A |
G |
6: 97,153,770 (GRCm39) |
L101P |
probably damaging |
Het |
Tnni1 |
A |
G |
1: 135,733,330 (GRCm39) |
T51A |
probably benign |
Het |
Tor3a |
T |
G |
1: 156,501,763 (GRCm39) |
E38A |
probably damaging |
Het |
Trim31 |
T |
A |
17: 37,210,810 (GRCm39) |
D147E |
possibly damaging |
Het |
Vmn1r48 |
G |
T |
6: 90,013,129 (GRCm39) |
A232E |
probably benign |
Het |
Vmn1r89 |
T |
G |
7: 12,953,284 (GRCm39) |
F7V |
probably benign |
Het |
Zfp160 |
A |
G |
17: 21,247,114 (GRCm39) |
T555A |
probably benign |
Het |
Zfp981 |
C |
A |
4: 146,621,462 (GRCm39) |
T129K |
probably benign |
Het |
Zfpm2 |
T |
A |
15: 40,733,938 (GRCm39) |
F106I |
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 |
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'- AATGAACCCTGCCGAAGTC -3'
(R):5'- TGAGAGTCACCCAGTCATCC -3'
Sequencing Primer
(F):5'- TGCCGAAGTCCAATGCTG -3'
(R):5'- GAGAGTCACCCAGTCATCCTTTAATC -3'
|
Posted On |
2016-08-04 |