Incidental Mutation 'R1220:Yrdc'
| ID |
99989 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Yrdc
|
| Ensembl Gene |
ENSMUSG00000028889 |
| Gene Name |
yrdC domain containing (E.coli) |
| Synonyms |
IRIP |
| MMRRC Submission |
039289-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably essential
(E-score: 0.962)
|
| Stock # |
R1220 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
4 |
| Chromosomal Location |
124744552-124749035 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
T to A
at 124748329 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Serine to Threonine
at position 278
(S278T)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000099688
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000030723]
[ENSMUST00000064444]
[ENSMUST00000102628]
[ENSMUST00000106190]
[ENSMUST00000137769]
[ENSMUST00000144851]
[ENSMUST00000185036]
[ENSMUST00000163946]
|
| AlphaFold |
Q3U5F4 |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000030723
|
| SMART Domains |
Protein: ENSMUSP00000030723
Gene: ENSMUSG00000028890
| Domain | Start | End | E-Value | Type |
|---|
|
ZnF_C2H2
|
139 |
163 |
1.22e-4 |
SMART |
|
ZnF_C2H2
|
169 |
193 |
6.42e-4 |
SMART |
|
ZnF_C2H2
|
199 |
223 |
2.4e-3 |
SMART |
|
ZnF_C2H2
|
228 |
252 |
2.57e-3 |
SMART |
|
ZnF_C2H2
|
258 |
282 |
2.57e-3 |
SMART |
|
ZnF_C2H2
|
288 |
312 |
7.37e-4 |
SMART |
|
low complexity region
|
429 |
456 |
N/A |
INTRINSIC |
|
low complexity region
|
500 |
526 |
N/A |
INTRINSIC |
|
low complexity region
|
545 |
558 |
N/A |
INTRINSIC |
|
low complexity region
|
628 |
638 |
N/A |
INTRINSIC |
|
low complexity region
|
656 |
669 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000064444
|
| SMART Domains |
Protein: ENSMUSP00000066000
Gene: ENSMUSG00000042763
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
25 |
N/A |
INTRINSIC |
|
low complexity region
|
31 |
46 |
N/A |
INTRINSIC |
|
low complexity region
|
55 |
79 |
N/A |
INTRINSIC |
|
Pfam:Glyco_hydro_99
|
95 |
445 |
8.7e-160 |
PFAM |
|
| Predicted Effect |
possibly damaging
Transcript: ENSMUST00000102628
AA Change: S278T
PolyPhen 2
Score 0.615 (Sensitivity: 0.87; Specificity: 0.91)
|
| SMART Domains |
Protein: ENSMUSP00000099688
Gene: ENSMUSG00000028889
AA Change: S278T
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
32 |
63 |
N/A |
INTRINSIC |
|
Pfam:Sua5_yciO_yrdC
|
76 |
256 |
1.3e-46 |
PFAM |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000106190
|
| SMART Domains |
Protein: ENSMUSP00000101796
Gene: ENSMUSG00000078570
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:DUF4726
|
10 |
110 |
2e-66 |
PFAM |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000125776
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000137769
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000144851
|
| SMART Domains |
Protein: ENSMUSP00000114150
Gene: ENSMUSG00000028889
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:Sua5_yciO_yrdC
|
1 |
103 |
2.5e-20 |
PFAM |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000173434
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000184704
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000185036
|
| SMART Domains |
Protein: ENSMUSP00000139121
Gene: ENSMUSG00000078570
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
66 |
89 |
N/A |
INTRINSIC |
|
low complexity region
|
123 |
137 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000163946
|
| Meta Mutation Damage Score |
0.1021 |
| Coding Region Coverage |
- 1x: 98.9%
- 3x: 97.9%
- 10x: 95.2%
- 20x: 89.2%
|
| Validation Efficiency |
100% (35/35) |
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 32 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Acsm1 |
C |
A |
7: 119,257,537 (GRCm39) |
S407R |
probably benign |
Het |
| Add2 |
A |
T |
6: 86,063,982 (GRCm39) |
M94L |
possibly damaging |
Het |
| Anks6 |
A |
T |
4: 47,025,767 (GRCm39) |
|
probably benign |
Het |
| Atxn1 |
A |
G |
13: 45,710,899 (GRCm39) |
S678P |
probably benign |
Het |
| Ccnc |
A |
G |
4: 21,732,491 (GRCm39) |
Y76C |
probably damaging |
Het |
| Col1a1 |
G |
T |
11: 94,841,957 (GRCm39) |
A1335S |
unknown |
Het |
| Col25a1 |
G |
T |
3: 130,182,574 (GRCm39) |
|
probably benign |
Het |
| Commd10 |
C |
A |
18: 47,220,107 (GRCm39) |
Q195K |
probably damaging |
Het |
| Cps1 |
G |
A |
1: 67,243,862 (GRCm39) |
|
probably null |
Het |
| Cramp1 |
A |
T |
17: 25,201,211 (GRCm39) |
V757D |
probably damaging |
Het |
| Cttn |
T |
C |
7: 144,017,699 (GRCm39) |
T13A |
probably benign |
Het |
| Eftud2 |
A |
G |
11: 102,742,573 (GRCm39) |
|
probably benign |
Het |
| Eif4enif1 |
A |
G |
11: 3,189,493 (GRCm39) |
|
probably benign |
Het |
| Exoc3l2 |
T |
A |
7: 19,225,709 (GRCm39) |
|
probably benign |
Het |
| Fam118b |
T |
C |
9: 35,134,969 (GRCm39) |
S213G |
possibly damaging |
Het |
| Katnal1 |
G |
A |
5: 148,831,061 (GRCm39) |
A171V |
probably benign |
Het |
| Lrig3 |
A |
G |
10: 125,832,945 (GRCm39) |
N273S |
probably damaging |
Het |
| Lrriq1 |
G |
A |
10: 102,906,990 (GRCm39) |
R1577W |
probably benign |
Het |
| Or1e26 |
A |
C |
11: 73,480,203 (GRCm39) |
Y120* |
probably null |
Het |
| Or5p70 |
T |
A |
7: 107,994,539 (GRCm39) |
S71T |
probably benign |
Het |
| Pmel |
A |
G |
10: 128,549,929 (GRCm39) |
D30G |
probably benign |
Het |
| Ppp1r15a |
T |
C |
7: 45,173,293 (GRCm39) |
Y505C |
probably damaging |
Het |
| Prpf40b |
C |
T |
15: 99,214,229 (GRCm39) |
R830C |
probably benign |
Het |
| Rabgap1l |
A |
T |
1: 160,566,479 (GRCm39) |
D106E |
probably damaging |
Het |
| Rad18 |
C |
A |
6: 112,626,625 (GRCm39) |
E141* |
probably null |
Het |
| Ros1 |
C |
T |
10: 51,974,966 (GRCm39) |
V1540M |
probably damaging |
Het |
| Secisbp2 |
G |
A |
13: 51,810,941 (GRCm39) |
R201H |
probably damaging |
Het |
| Shisa6 |
A |
G |
11: 66,110,836 (GRCm39) |
S302P |
probably damaging |
Het |
| Slamf9 |
C |
A |
1: 172,304,898 (GRCm39) |
Q171K |
probably benign |
Het |
| Sox6 |
T |
A |
7: 115,261,677 (GRCm39) |
T180S |
probably damaging |
Het |
| Ttn |
T |
C |
2: 76,553,998 (GRCm39) |
S30902G |
possibly damaging |
Het |
| Xirp1 |
A |
G |
9: 119,846,982 (GRCm39) |
F634L |
possibly damaging |
Het |
|
| Other mutations in Yrdc |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL00157:Yrdc
|
APN |
4 |
124,747,754 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL01142:Yrdc
|
APN |
4 |
124,747,787 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R0525:Yrdc
|
UTSW |
4 |
124,745,559 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1162:Yrdc
|
UTSW |
4 |
124,748,254 (GRCm39) |
unclassified |
probably benign |
|
|
R1952:Yrdc
|
UTSW |
4 |
124,745,739 (GRCm39) |
missense |
probably benign |
0.00 |
|
R3829:Yrdc
|
UTSW |
4 |
124,745,554 (GRCm39) |
start codon destroyed |
probably null |
0.92 |
|
R7121:Yrdc
|
UTSW |
4 |
124,744,748 (GRCm39) |
missense |
probably benign |
0.06 |
|
R7272:Yrdc
|
UTSW |
4 |
124,744,820 (GRCm39) |
missense |
probably benign |
0.23 |
|
R8169:Yrdc
|
UTSW |
4 |
124,744,880 (GRCm39) |
missense |
probably benign |
|
|
R8837:Yrdc
|
UTSW |
4 |
124,747,677 (GRCm39) |
missense |
probably benign |
0.01 |
|
R9159:Yrdc
|
UTSW |
4 |
124,747,811 (GRCm39) |
critical splice donor site |
probably null |
|
|
Z1176:Yrdc
|
UTSW |
4 |
124,745,290 (GRCm39) |
unclassified |
probably benign |
|
|
| Predicted Primers |
PCR Primer
(F):5'- GCTGCCACAGAGAGGTGTTAAGTG -3'
(R):5'- ACTTTGCTGCGTTGGTCCTAAGAC -3'
Sequencing Primer
(F):5'- CTGGGACTAAATTTGCTGGTATAG -3'
(R):5'- TGTCACTGTTCCCCAGAAAG -3'
|
| Posted On |
2014-01-15 |
Incidental Mutation