Incidental Mutation 'R0944:Pdxdc1'
| ID |
82029 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Pdxdc1
|
| Ensembl Gene |
ENSMUSG00000022680 |
| Gene Name |
pyridoxal-dependent decarboxylase domain containing 1 |
| Synonyms |
2210010A19Rik |
| MMRRC Submission |
039083-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably non essential
(E-score: 0.192)
|
| Stock # |
R0944 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
16 |
| Chromosomal Location |
13651012-13720995 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to G
at 13656233 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Valine to Alanine
at position 613
(V613A)
|
| 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 damaging
Transcript: ENSMUST00000023361
AA Change: V613A
PolyPhen 2
Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)
|
| SMART Domains |
Protein: ENSMUSP00000023361
Gene: ENSMUSG00000022680
AA Change: V613A
| 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 damaging
Transcript: ENSMUST00000115804
AA Change: V613A
PolyPhen 2
Score 0.991 (Sensitivity: 0.71; Specificity: 0.97)
|
| SMART Domains |
Protein: ENSMUSP00000111471
Gene: ENSMUSG00000022680
AA Change: V613A
| 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: ENSMUST00000150435
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000148848
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000144913
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000152450
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000154150
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000139161
|
| Meta Mutation Damage Score |
0.5633 |
| Coding Region Coverage |
- 1x: 99.7%
- 3x: 99.1%
- 10x: 97.3%
- 20x: 94.3%
|
| Validation Efficiency |
100% (51/51) |
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 50 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 3110018I06Rik |
G |
A |
12: 107,455,268 (GRCm39) |
R118K |
unknown |
Het |
| Abcc6 |
T |
A |
7: 45,664,929 (GRCm39) |
I301F |
possibly damaging |
Het |
| Akap9 |
C |
A |
5: 4,114,742 (GRCm39) |
|
probably null |
Het |
| Alg6 |
A |
G |
4: 99,650,297 (GRCm39) |
I506V |
probably benign |
Het |
| B3gat1 |
C |
T |
9: 26,668,237 (GRCm39) |
R276C |
probably damaging |
Het |
| Camk1 |
A |
G |
6: 113,315,352 (GRCm39) |
Y105H |
probably damaging |
Het |
| Ccdc81 |
T |
C |
7: 89,515,777 (GRCm39) |
N634S |
probably damaging |
Het |
| Clcn1 |
C |
A |
6: 42,290,075 (GRCm39) |
Q837K |
probably benign |
Het |
| Clec16a |
A |
G |
16: 10,506,510 (GRCm39) |
|
probably benign |
Het |
| Col22a1 |
T |
C |
15: 71,753,511 (GRCm39) |
I130V |
probably benign |
Het |
| Coro2b |
T |
C |
9: 62,335,263 (GRCm39) |
S308G |
probably benign |
Het |
| Cpxm1 |
A |
G |
2: 130,239,423 (GRCm39) |
W2R |
probably damaging |
Het |
| Csmd3 |
T |
C |
15: 47,475,227 (GRCm39) |
N3364S |
probably damaging |
Het |
| Dgkq |
A |
G |
5: 108,804,331 (GRCm39) |
V131A |
probably damaging |
Het |
| Dnai1 |
A |
G |
4: 41,629,997 (GRCm39) |
S469G |
probably benign |
Het |
| Efcab3 |
T |
G |
11: 104,601,556 (GRCm39) |
|
probably null |
Het |
| Eml4 |
G |
A |
17: 83,785,489 (GRCm39) |
E885K |
probably benign |
Het |
| Etfa |
A |
T |
9: 55,396,122 (GRCm39) |
I148N |
probably damaging |
Het |
| Gpbar1 |
A |
G |
1: 74,318,681 (GRCm39) |
D308G |
probably benign |
Het |
| Gprin3 |
T |
C |
6: 59,330,900 (GRCm39) |
E469G |
possibly damaging |
Het |
| Igkv1-115 |
T |
C |
6: 68,138,667 (GRCm39) |
V90A |
probably damaging |
Het |
| Ints2 |
A |
G |
11: 86,135,289 (GRCm39) |
V375A |
possibly damaging |
Het |
| Mindy3 |
T |
C |
2: 12,400,993 (GRCm39) |
M242V |
possibly damaging |
Het |
| Or11m3 |
A |
G |
15: 98,395,565 (GRCm39) |
I71V |
probably benign |
Het |
| Or1n1b |
T |
C |
2: 36,780,698 (GRCm39) |
H54R |
probably damaging |
Het |
| Or5t9 |
A |
C |
2: 86,659,281 (GRCm39) |
I62L |
probably benign |
Het |
| P3h1 |
G |
A |
4: 119,095,956 (GRCm39) |
E355K |
probably benign |
Het |
| Paxbp1 |
T |
C |
16: 90,820,315 (GRCm39) |
T703A |
probably benign |
Het |
| Pcdh15 |
A |
T |
10: 74,046,302 (GRCm39) |
Y193F |
probably damaging |
Het |
| Plekha5 |
T |
C |
6: 140,515,922 (GRCm39) |
|
probably benign |
Het |
| Pmel |
A |
T |
10: 128,551,126 (GRCm39) |
Q123L |
possibly damaging |
Het |
| Prl6a1 |
T |
C |
13: 27,502,149 (GRCm39) |
|
probably benign |
Het |
| Rcan1 |
T |
C |
16: 92,190,379 (GRCm39) |
T187A |
probably damaging |
Het |
| Rp1l1 |
A |
G |
14: 64,269,681 (GRCm39) |
S1756G |
probably benign |
Het |
| Runx2 |
A |
T |
17: 44,919,123 (GRCm39) |
M405K |
probably damaging |
Het |
| Serinc5 |
T |
C |
13: 92,797,613 (GRCm39) |
Y39H |
probably damaging |
Het |
| Sgsm1 |
G |
A |
5: 113,413,740 (GRCm39) |
T676I |
probably benign |
Het |
| Slc6a15 |
G |
C |
10: 103,245,657 (GRCm39) |
V547L |
probably benign |
Het |
| Slk |
T |
C |
19: 47,597,432 (GRCm39) |
I80T |
probably damaging |
Het |
| Spice1 |
A |
G |
16: 44,205,124 (GRCm39) |
N810S |
probably benign |
Het |
| Spred2 |
A |
G |
11: 19,951,104 (GRCm39) |
|
probably benign |
Het |
| Tbc1d4 |
C |
G |
14: 101,716,656 (GRCm39) |
|
probably benign |
Het |
| Tdrd7 |
G |
A |
4: 46,029,762 (GRCm39) |
V1032M |
probably benign |
Het |
| Tlr11 |
A |
G |
14: 50,599,793 (GRCm39) |
N593S |
probably benign |
Het |
| Trpa1 |
T |
C |
1: 14,982,585 (GRCm39) |
|
probably null |
Het |
| Ugcg |
C |
T |
4: 59,207,798 (GRCm39) |
P46S |
probably benign |
Het |
| Usp25 |
T |
C |
16: 76,878,335 (GRCm39) |
|
probably benign |
Het |
| Vmn2r97 |
T |
A |
17: 19,167,665 (GRCm39) |
S640T |
probably benign |
Het |
| Zc3h6 |
A |
G |
2: 128,848,736 (GRCm39) |
Y321C |
probably damaging |
Het |
| Zfp329 |
T |
A |
7: 12,545,395 (GRCm39) |
N43I |
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 |
|
|
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'- AGCCTGGACTGGAGAAAACCAATTC -3'
(R):5'- TTGGCAAATGAGGCCGGACAAC -3'
Sequencing Primer
(F):5'- GATCCTACTACAGGGATTTGCCG -3'
(R):5'- CCGGACAACAGGTTATATGTGC -3'
|
| Posted On |
2013-11-08 |
Incidental Mutation