Incidental Mutation 'R3082:L2hgdh'
| ID |
265497 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
L2hgdh
|
| Ensembl Gene |
ENSMUSG00000020988 |
| Gene Name |
L-2-hydroxyglutarate dehydrogenase |
| Synonyms |
|
| MMRRC Submission |
040572-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably non essential
(E-score: 0.221)
|
| Stock # |
R3082 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
12 |
| Chromosomal Location |
69737210-69771648 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
C to T
at 69768858 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Aspartic acid to Asparagine
at position 85
(D85N)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000021370
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000021370]
[ENSMUST00000021372]
[ENSMUST00000220460]
[ENSMUST00000220539]
[ENSMUST00000220916]
[ENSMUST00000222950]
|
| AlphaFold |
Q91YP0 |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000021370
AA Change: D85N
PolyPhen 2
Score 0.002 (Sensitivity: 0.99; Specificity: 0.30)
|
| SMART Domains |
Protein: ENSMUSP00000021370
Gene: ENSMUSG00000020988
AA Change: D85N
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
39 |
49 |
N/A |
INTRINSIC |
|
Pfam:DAO
|
51 |
457 |
1.9e-72 |
PFAM |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000021372
|
| SMART Domains |
Protein: ENSMUSP00000021372
Gene: ENSMUSG00000054894
| Domain | Start | End | E-Value | Type |
|---|
|
PDB:3E4G|A
|
26 |
200 |
1e-102 |
PDB |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000220460
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000220539
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000220916
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000222950
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000222972
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000223387
|
| Meta Mutation Damage Score |
0.1018 |
| Coding Region Coverage |
- 1x: 99.2%
- 3x: 98.7%
- 10x: 97.5%
- 20x: 95.7%
|
| Validation Efficiency |
100% (44/44) |
| MGI Phenotype |
FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes L-2-hydroxyglutarate dehydrogenase, a FAD-dependent enzyme that oxidizes L-2-hydroxyglutarate to alpha-ketoglutarate in a variety of mammalian tissues. Mutations in this gene cause L-2-hydroxyglutaric aciduria, a rare autosomal recessive neurometabolic disorder resulting in moderate to severe mental retardation. [provided by RefSeq, Jul 2008]
PHENOTYPE: Mice homozygous for a hypomorphic allele exhibit increased levels of lysine and arginine associated with decreases in saccharopine, glutamine, and glutamate in adult brains, neurobehavioral deficits, and brain spongiosis with vacuolar lesions mostly affecting oligodendrocytes and myelin sheaths. [provided by MGI curators]
|
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 42 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Acss3 |
A |
G |
10: 106,859,576 (GRCm39) |
V341A |
possibly damaging |
Het |
| Adam11 |
T |
C |
11: 102,660,943 (GRCm39) |
|
probably benign |
Het |
| Aox1 |
G |
T |
1: 58,322,759 (GRCm39) |
|
probably benign |
Het |
| Cdh6 |
T |
C |
15: 13,044,838 (GRCm39) |
D428G |
probably damaging |
Het |
| Cep63 |
T |
C |
9: 102,479,696 (GRCm39) |
T339A |
probably benign |
Het |
| Clcn1 |
T |
C |
6: 42,267,112 (GRCm39) |
Y66H |
probably damaging |
Het |
| Cpsf2 |
C |
G |
12: 101,955,069 (GRCm39) |
S280C |
probably damaging |
Het |
| Dcaf6 |
G |
T |
1: 165,250,421 (GRCm39) |
|
probably benign |
Het |
| Ddx39a |
T |
A |
8: 84,449,335 (GRCm39) |
N344K |
possibly damaging |
Het |
| Dvl1 |
T |
C |
4: 155,932,316 (GRCm39) |
V42A |
possibly damaging |
Het |
| Ep400 |
A |
G |
5: 110,841,096 (GRCm39) |
|
probably benign |
Het |
| Epb41l5 |
C |
T |
1: 119,536,992 (GRCm39) |
V300I |
probably damaging |
Het |
| Fbln1 |
T |
G |
15: 85,149,454 (GRCm39) |
I617S |
probably benign |
Het |
| Gas2l3 |
CACTCGTCATACT |
CACT |
10: 89,266,820 (GRCm39) |
|
probably benign |
Het |
| Grin3a |
G |
A |
4: 49,665,243 (GRCm39) |
R1131W |
probably benign |
Het |
| Incenp |
T |
A |
19: 9,861,143 (GRCm39) |
M480L |
unknown |
Het |
| Ints13 |
G |
T |
6: 146,476,205 (GRCm39) |
Q99K |
possibly damaging |
Het |
| Lct |
A |
G |
1: 128,215,345 (GRCm39) |
Y1744H |
probably damaging |
Het |
| Macf1 |
T |
C |
4: 123,255,236 (GRCm39) |
|
probably null |
Het |
| Mpdz |
A |
T |
4: 81,203,695 (GRCm39) |
|
probably benign |
Het |
| Naa15 |
T |
C |
3: 51,367,471 (GRCm39) |
L498P |
probably damaging |
Het |
| Naip6 |
T |
A |
13: 100,452,925 (GRCm39) |
E45D |
probably benign |
Het |
| Nedd4l |
T |
A |
18: 65,312,049 (GRCm39) |
N405K |
probably benign |
Het |
| Or4l15 |
A |
G |
14: 50,198,161 (GRCm39) |
Y123H |
probably damaging |
Het |
| Or8u10 |
C |
T |
2: 85,916,053 (GRCm39) |
V23I |
probably benign |
Het |
| Pitpnc1 |
A |
G |
11: 107,103,350 (GRCm39) |
S250P |
possibly damaging |
Het |
| Ppp1r18 |
A |
G |
17: 36,184,742 (GRCm39) |
D131G |
probably damaging |
Het |
| Prdm5 |
A |
G |
6: 65,913,069 (GRCm39) |
D206G |
probably damaging |
Het |
| Pygl |
A |
G |
12: 70,244,303 (GRCm39) |
F455S |
probably damaging |
Het |
| Rictor |
A |
T |
15: 6,804,338 (GRCm39) |
Y565F |
probably benign |
Het |
| Ryr1 |
T |
C |
7: 28,745,071 (GRCm39) |
N3852D |
probably damaging |
Het |
| S1pr5 |
A |
T |
9: 21,156,286 (GRCm39) |
C47S |
probably damaging |
Het |
| Serpinf2 |
T |
C |
11: 75,328,354 (GRCm39) |
R65G |
probably benign |
Het |
| Slfn14 |
C |
T |
11: 83,167,519 (GRCm39) |
W665* |
probably null |
Het |
| Smu1 |
T |
C |
4: 40,745,567 (GRCm39) |
D251G |
probably damaging |
Het |
| Spata18 |
A |
G |
5: 73,836,423 (GRCm39) |
|
probably benign |
Het |
| Tex19.2 |
A |
G |
11: 121,007,557 (GRCm39) |
V297A |
probably benign |
Het |
| Tmem131l |
A |
G |
3: 83,816,457 (GRCm39) |
|
probably null |
Het |
| Trim9 |
T |
C |
12: 70,301,887 (GRCm39) |
R584G |
possibly damaging |
Het |
| Trpm7 |
A |
T |
2: 126,686,342 (GRCm39) |
N295K |
possibly damaging |
Het |
| Ugt2a3 |
A |
G |
5: 87,473,534 (GRCm39) |
V461A |
probably benign |
Het |
| Vmn1r45 |
A |
T |
6: 89,910,724 (GRCm39) |
M82K |
probably benign |
Het |
|
| Other mutations in L2hgdh |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL00158:L2hgdh
|
APN |
12 |
69,748,208 (GRCm39) |
missense |
possibly damaging |
0.67 |
|
IGL01505:L2hgdh
|
APN |
12 |
69,768,175 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL01871:L2hgdh
|
APN |
12 |
69,768,869 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL02169:L2hgdh
|
APN |
12 |
69,768,171 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL02253:L2hgdh
|
APN |
12 |
69,752,534 (GRCm39) |
splice site |
probably benign |
|
|
IGL02670:L2hgdh
|
APN |
12 |
69,739,254 (GRCm39) |
missense |
possibly damaging |
0.86 |
|
IGL03069:L2hgdh
|
APN |
12 |
69,739,173 (GRCm39) |
missense |
probably benign |
|
|
R0054:L2hgdh
|
UTSW |
12 |
69,768,105 (GRCm39) |
missense |
possibly damaging |
0.82 |
|
R0106:L2hgdh
|
UTSW |
12 |
69,752,563 (GRCm39) |
nonsense |
probably null |
|
|
R0106:L2hgdh
|
UTSW |
12 |
69,752,563 (GRCm39) |
nonsense |
probably null |
|
|
R0579:L2hgdh
|
UTSW |
12 |
69,748,046 (GRCm39) |
splice site |
probably benign |
|
|
R1421:L2hgdh
|
UTSW |
12 |
69,748,092 (GRCm39) |
missense |
probably benign |
|
|
R1797:L2hgdh
|
UTSW |
12 |
69,746,340 (GRCm39) |
missense |
probably benign |
|
|
R7640:L2hgdh
|
UTSW |
12 |
69,768,131 (GRCm39) |
nonsense |
probably null |
|
|
R9087:L2hgdh
|
UTSW |
12 |
69,749,131 (GRCm39) |
missense |
probably benign |
|
|
R9582:L2hgdh
|
UTSW |
12 |
69,739,172 (GRCm39) |
missense |
probably benign |
0.02 |
|
Z1176:L2hgdh
|
UTSW |
12 |
69,753,906 (GRCm39) |
missense |
probably benign |
0.02 |
|
| Predicted Primers |
PCR Primer
(F):5'- TGGACCCTCCTGTGGATTTC -3'
(R):5'- GTGAAGTTTGGTGAGGTCTATAAAC -3'
Sequencing Primer
(F):5'- ACCCCCTCCCTTCTTCCTAC -3'
(R):5'- ACTACAGATGGTTGTGAGTCACC -3'
|
| Posted On |
2015-02-05 |
Incidental Mutation