Incidental Mutation 'R6711:Ndrg2'
| ID |
529147 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Ndrg2
|
| Ensembl Gene |
ENSMUSG00000004558 |
| Gene Name |
N-myc downstream regulated gene 2 |
| Synonyms |
Ndr2 |
| MMRRC Submission |
044829-MU
|
| Accession Numbers |
|
| Essential gene? |
Possibly non essential
(E-score: 0.483)
|
| Stock # |
R6711 (G1)
|
| Quality Score |
225.009 |
|
Status
|
Validated
|
| Chromosome |
14 |
| Chromosomal Location |
52142728-52151461 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to T
at 52147782 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Phenylalanine to Isoleucine
at position 112
(F112I)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000004673
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000004673]
[ENSMUST00000111632]
[ENSMUST00000226184]
[ENSMUST00000226528]
[ENSMUST00000227402]
[ENSMUST00000227237]
[ENSMUST00000228164]
|
| AlphaFold |
Q9QYG0 |
| PDB Structure |
Crystal structure of a n-myc downstream regulated 2 protein (ndrg2, syld, ndr2, ai182517, au040374) from mus musculus at 1.70 A resolution [X-RAY DIFFRACTION]
|
| Predicted Effect |
possibly damaging
Transcript: ENSMUST00000004673
AA Change: F112I
PolyPhen 2
Score 0.939 (Sensitivity: 0.80; Specificity: 0.94)
|
| SMART Domains |
Protein: ENSMUSP00000004673
Gene: ENSMUSG00000004558
AA Change: F112I
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:Ndr
|
40 |
318 |
5.4e-125 |
PFAM |
|
low complexity region
|
323 |
338 |
N/A |
INTRINSIC |
|
low complexity region
|
342 |
355 |
N/A |
INTRINSIC |
|
| Predicted Effect |
possibly damaging
Transcript: ENSMUST00000111632
AA Change: F98I
PolyPhen 2
Score 0.923 (Sensitivity: 0.81; Specificity: 0.94)
|
| SMART Domains |
Protein: ENSMUSP00000107259
Gene: ENSMUSG00000004558
AA Change: F98I
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:Ndr
|
26 |
304 |
4.7e-125 |
PFAM |
|
Pfam:Abhydrolase_6
|
58 |
292 |
7.6e-11 |
PFAM |
|
low complexity region
|
309 |
324 |
N/A |
INTRINSIC |
|
low complexity region
|
328 |
341 |
N/A |
INTRINSIC |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000226122
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000226184
AA Change: F112I
PolyPhen 2
Score 0.101 (Sensitivity: 0.93; Specificity: 0.86)
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000226364
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000226366
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000226528
AA Change: F98I
PolyPhen 2
Score 0.074 (Sensitivity: 0.93; Specificity: 0.85)
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000227402
AA Change: F112I
PolyPhen 2
Score 0.272 (Sensitivity: 0.91; Specificity: 0.88)
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000227237
AA Change: F98I
PolyPhen 2
Score 0.286 (Sensitivity: 0.91; Specificity: 0.88)
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000228164
AA Change: F98I
PolyPhen 2
Score 0.063 (Sensitivity: 0.94; Specificity: 0.84)
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000226698
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000228620
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000228173
|
| Coding Region Coverage |
- 1x: 99.9%
- 3x: 99.6%
- 10x: 98.1%
- 20x: 94.5%
|
| Validation Efficiency |
100% (47/47) |
| MGI Phenotype |
FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene is a member of the N-myc downregulated gene family which belongs to the alpha/beta hydrolase superfamily. The protein encoded by this gene is a cytoplasmic protein that may play a role in neurite outgrowth. This gene may be involved in glioblastoma carcinogenesis. Several alternatively spliced transcript variants of this gene have been described, but the full-length nature of some of these variants has not been determined. [provided by RefSeq, Jul 2008]
PHENOTYPE: Mice homozygous for a null allele develop various types of tumors, including T-cell lymphomas, and have a shorter lifespan. Homozygotes for a second null allele show vertebral transformations. Homozygotes for a third null allele show reduced astrogliosis and inflammatory response after brain injury. [provided by MGI curators]
|
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 46 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Akr1c21 |
A |
G |
13: 4,627,374 (GRCm39) |
D156G |
probably damaging |
Het |
| Ankrd35 |
C |
T |
3: 96,590,784 (GRCm39) |
Q357* |
probably null |
Het |
| Ano2 |
G |
A |
6: 125,752,795 (GRCm39) |
A191T |
probably damaging |
Het |
| Cacna2d1 |
C |
T |
5: 16,505,039 (GRCm39) |
T331I |
probably damaging |
Het |
| Ccdc81 |
T |
G |
7: 89,537,006 (GRCm39) |
E214A |
probably damaging |
Het |
| Cdh4 |
A |
G |
2: 179,532,724 (GRCm39) |
T729A |
probably damaging |
Het |
| Ceacam2 |
A |
G |
7: 25,238,295 (GRCm39) |
L43P |
probably benign |
Het |
| Ces2h |
A |
T |
8: 105,744,715 (GRCm39) |
R364S |
probably benign |
Het |
| Dcpp3 |
AGGCCATGCTGGCC |
AGGCC |
17: 24,136,572 (GRCm39) |
|
probably benign |
Het |
| Entrep1 |
T |
C |
19: 23,955,463 (GRCm39) |
N385S |
probably benign |
Het |
| Epb42 |
T |
A |
2: 120,854,589 (GRCm39) |
|
probably benign |
Het |
| Fcgbp |
G |
A |
7: 27,789,098 (GRCm39) |
V555M |
probably damaging |
Het |
| Ganc |
A |
T |
2: 120,281,320 (GRCm39) |
H723L |
possibly damaging |
Het |
| Gfra2 |
A |
G |
14: 71,203,715 (GRCm39) |
D31G |
probably damaging |
Het |
| Glrb |
A |
G |
3: 80,752,281 (GRCm39) |
I443T |
probably benign |
Het |
| Hcfc1 |
A |
T |
X: 72,993,671 (GRCm39) |
C1165S |
probably damaging |
Homo |
| Hoxd10 |
A |
G |
2: 74,524,507 (GRCm39) |
Y273C |
probably damaging |
Het |
| Iba57 |
T |
C |
11: 59,049,369 (GRCm39) |
T267A |
probably damaging |
Het |
| Impg2 |
C |
A |
16: 56,085,449 (GRCm39) |
P943H |
probably damaging |
Het |
| Kidins220 |
A |
G |
12: 25,048,750 (GRCm39) |
T145A |
probably damaging |
Het |
| Lmntd1 |
T |
C |
6: 145,489,228 (GRCm39) |
Y11C |
probably benign |
Het |
| Lyst |
A |
T |
13: 13,809,820 (GRCm39) |
T497S |
possibly damaging |
Het |
| Man1a |
G |
A |
10: 53,809,588 (GRCm39) |
H406Y |
probably benign |
Het |
| Mme |
A |
T |
3: 63,249,339 (GRCm39) |
K289N |
possibly damaging |
Het |
| Mrps21 |
G |
A |
3: 95,777,895 (GRCm39) |
|
probably benign |
Het |
| Mtor |
A |
G |
4: 148,536,824 (GRCm39) |
N33D |
possibly damaging |
Het |
| Ncoa1 |
C |
A |
12: 4,372,904 (GRCm39) |
A166S |
probably benign |
Het |
| Neb |
A |
C |
2: 52,113,076 (GRCm39) |
F36C |
probably benign |
Het |
| Neb |
A |
G |
2: 52,146,299 (GRCm39) |
Y2893H |
probably damaging |
Het |
| Or8g22 |
A |
G |
9: 38,958,162 (GRCm39) |
*229Q |
probably null |
Het |
| Pcdh15 |
A |
T |
10: 74,478,219 (GRCm39) |
E231D |
possibly damaging |
Het |
| Pih1d2 |
T |
A |
9: 50,529,310 (GRCm39) |
M1K |
probably null |
Het |
| Pla2g4e |
T |
C |
2: 120,001,751 (GRCm39) |
N633D |
probably benign |
Het |
| Rph3al |
C |
A |
11: 75,799,810 (GRCm39) |
G50* |
probably null |
Het |
| Rtcb |
A |
T |
10: 85,774,963 (GRCm39) |
N477K |
possibly damaging |
Het |
| Scn10a |
A |
G |
9: 119,438,979 (GRCm39) |
F1630S |
probably damaging |
Het |
| Srfbp1 |
T |
C |
18: 52,621,373 (GRCm39) |
S145P |
probably damaging |
Het |
| St7 |
A |
G |
6: 17,848,069 (GRCm39) |
E211G |
possibly damaging |
Het |
| Thbs2 |
T |
C |
17: 14,910,527 (GRCm39) |
D24G |
probably benign |
Het |
| Tlr6 |
C |
A |
5: 65,111,835 (GRCm39) |
M357I |
probably damaging |
Het |
| Tmem168 |
T |
C |
6: 13,603,120 (GRCm39) |
Y82C |
probably damaging |
Het |
| Tnrc18 |
A |
T |
5: 142,773,545 (GRCm39) |
L245Q |
unknown |
Het |
| Vmn1r8 |
T |
C |
6: 57,013,444 (GRCm39) |
L165P |
probably damaging |
Het |
| Vps13b |
A |
G |
15: 35,887,395 (GRCm39) |
Y3268C |
probably damaging |
Het |
| Zdhhc7 |
A |
G |
8: 120,810,066 (GRCm39) |
I218T |
probably benign |
Het |
| Zfp213 |
A |
G |
17: 23,778,485 (GRCm39) |
F209S |
probably benign |
Het |
|
| Other mutations in Ndrg2 |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL02261:Ndrg2
|
APN |
14 |
52,148,566 (GRCm39) |
missense |
probably damaging |
0.99 |
|
IGL02645:Ndrg2
|
APN |
14 |
52,143,979 (GRCm39) |
missense |
possibly damaging |
0.87 |
|
IGL03226:Ndrg2
|
APN |
14 |
52,144,026 (GRCm39) |
unclassified |
probably benign |
|
|
R0015:Ndrg2
|
UTSW |
14 |
52,147,902 (GRCm39) |
splice site |
probably benign |
|
|
R0015:Ndrg2
|
UTSW |
14 |
52,147,902 (GRCm39) |
splice site |
probably benign |
|
|
R0197:Ndrg2
|
UTSW |
14 |
52,144,460 (GRCm39) |
unclassified |
probably benign |
|
|
R0606:Ndrg2
|
UTSW |
14 |
52,143,674 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R0812:Ndrg2
|
UTSW |
14 |
52,146,119 (GRCm39) |
splice site |
probably benign |
|
|
R1449:Ndrg2
|
UTSW |
14 |
52,145,591 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1625:Ndrg2
|
UTSW |
14 |
52,144,420 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R3803:Ndrg2
|
UTSW |
14 |
52,148,132 (GRCm39) |
splice site |
probably null |
|
|
R5242:Ndrg2
|
UTSW |
14 |
52,148,541 (GRCm39) |
critical splice donor site |
probably null |
|
|
R5424:Ndrg2
|
UTSW |
14 |
52,146,342 (GRCm39) |
missense |
probably damaging |
0.97 |
|
R5568:Ndrg2
|
UTSW |
14 |
52,144,420 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5703:Ndrg2
|
UTSW |
14 |
52,147,579 (GRCm39) |
critical splice acceptor site |
probably null |
|
|
R7515:Ndrg2
|
UTSW |
14 |
52,146,380 (GRCm39) |
missense |
probably benign |
0.40 |
|
R7689:Ndrg2
|
UTSW |
14 |
52,147,812 (GRCm39) |
missense |
possibly damaging |
0.53 |
|
R7934:Ndrg2
|
UTSW |
14 |
52,143,661 (GRCm39) |
missense |
probably benign |
0.01 |
|
R9520:Ndrg2
|
UTSW |
14 |
52,146,381 (GRCm39) |
missense |
probably benign |
|
|
R9689:Ndrg2
|
UTSW |
14 |
52,146,071 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9738:Ndrg2
|
UTSW |
14 |
52,148,238 (GRCm39) |
missense |
possibly damaging |
0.86 |
|
| Predicted Primers |
PCR Primer
(F):5'- CAGAGATGGGTACTGATATCTGG -3'
(R):5'- TAGTGTGGTGGCATCAGAGC -3'
Sequencing Primer
(F):5'- AGAGGAAAATACTAGTTACCAGTCTG -3'
(R):5'- CAAGAGGGTGGGTTCTGAC -3'
|
| Posted On |
2018-07-24 |
Incidental Mutation