Incidental Mutation 'R0080:D2hgdh'
| ID |
19632 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
D2hgdh
|
| Ensembl Gene |
ENSMUSG00000073609 |
| Gene Name |
D-2-hydroxyglutarate dehydrogenase |
| Synonyms |
|
| MMRRC Submission |
038367-MU
|
| Accession Numbers |
|
| Essential gene? |
Possibly non essential
(E-score: 0.266)
|
| Stock # |
R0080 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
1 |
| Chromosomal Location |
93752631-93780070 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to G
at 93754177 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Tyrosine to Cysteine
at position 50
(Y50C)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000140181
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000027505]
[ENSMUST00000097633]
[ENSMUST00000112881]
[ENSMUST00000187321]
[ENSMUST00000189154]
[ENSMUST00000188402]
[ENSMUST00000188532]
|
| AlphaFold |
Q8CIM3 |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000027505
|
| SMART Domains |
Protein: ENSMUSP00000027505
Gene: ENSMUSG00000026283
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:ING
|
6 |
107 |
1.6e-34 |
PFAM |
|
low complexity region
|
129 |
150 |
N/A |
INTRINSIC |
|
PHD
|
188 |
233 |
7.34e-12 |
SMART |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000097633
AA Change: Y50C
PolyPhen 2
Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
|
| SMART Domains |
Protein: ENSMUSP00000095235
Gene: ENSMUSG00000073609
AA Change: Y50C
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:FAD_binding_4
|
114 |
253 |
2.7e-35 |
PFAM |
|
Pfam:FAD-oxidase_C
|
289 |
530 |
7.3e-58 |
PFAM |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000112881
AA Change: Y72C
PolyPhen 2
Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
|
| SMART Domains |
Protein: ENSMUSP00000108502
Gene: ENSMUSG00000073609
AA Change: Y72C
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
20 |
N/A |
INTRINSIC |
|
Pfam:FAD_binding_4
|
136 |
275 |
7e-36 |
PFAM |
|
Pfam:FAD-oxidase_C
|
311 |
552 |
4.1e-61 |
PFAM |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000141701
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000149397
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000186783
|
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000187321
AA Change: Y50C
PolyPhen 2
Score 0.974 (Sensitivity: 0.76; Specificity: 0.96)
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000189154
AA Change: Y50C
PolyPhen 2
Score 0.002 (Sensitivity: 0.99; Specificity: 0.30)
|
| SMART Domains |
Protein: ENSMUSP00000140506
Gene: ENSMUSG00000073609
AA Change: Y50C
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:FAD_binding_4
|
114 |
179 |
3.2e-10 |
PFAM |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000188402
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000188532
|
| Meta Mutation Damage Score |
0.6467 |
| Coding Region Coverage |
- 1x: 99.1%
- 3x: 97.6%
- 10x: 93.1%
- 20x: 79.7%
|
| Validation Efficiency |
88% (175/200) |
| MGI Phenotype |
FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes D-2hydroxyglutarate dehydrogenase, a mitochondrial enzyme belonging to the FAD-binding oxidoreductase/transferase type 4 family. This enzyme, which is most active in liver and kidney but also active in heart and brain, converts D-2-hydroxyglutarate to 2-ketoglutarate. Mutations in this gene are present in D-2-hydroxyglutaric aciduria, a rare recessive neurometabolic disorder causing developmental delay, epilepsy, hypotonia, and dysmorphic features. [provided by RefSeq, Jul 2008]
|
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 43 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 4732465J04Rik |
GATCTATCTATCTATCTATCTATCTATCTATCTATCTATC |
GATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATC |
10: 95,630,440 (GRCm39) |
|
probably null |
Het |
| Adam17 |
A |
C |
12: 21,379,049 (GRCm39) |
|
probably benign |
Het |
| Adcy1 |
T |
C |
11: 7,099,497 (GRCm39) |
|
probably benign |
Het |
| Adgb |
T |
C |
10: 10,253,583 (GRCm39) |
|
probably benign |
Het |
| Antkmt |
T |
C |
17: 26,010,548 (GRCm39) |
I89V |
probably benign |
Het |
| Ccdc180 |
A |
G |
4: 45,896,205 (GRCm39) |
D118G |
probably null |
Het |
| Coro7 |
A |
T |
16: 4,448,328 (GRCm39) |
L714Q |
probably damaging |
Het |
| Dsg1b |
T |
G |
18: 20,530,424 (GRCm39) |
S360A |
probably damaging |
Het |
| Ednra |
T |
C |
8: 78,401,688 (GRCm39) |
I201V |
probably benign |
Het |
| Ggt6 |
A |
G |
11: 72,328,021 (GRCm39) |
T136A |
possibly damaging |
Het |
| Gnb5 |
A |
T |
9: 75,221,636 (GRCm39) |
E28V |
possibly damaging |
Het |
| Golgb1 |
T |
C |
16: 36,718,973 (GRCm39) |
L293P |
probably damaging |
Het |
| Gpr179 |
A |
G |
11: 97,242,295 (GRCm39) |
V183A |
probably benign |
Het |
| Grk6 |
T |
C |
13: 55,606,723 (GRCm39) |
S474P |
probably benign |
Het |
| Hectd4 |
A |
G |
5: 121,487,435 (GRCm39) |
S3477G |
probably benign |
Het |
| Hoatz |
T |
C |
9: 51,013,102 (GRCm39) |
T57A |
probably benign |
Het |
| Irx3 |
T |
C |
8: 92,526,954 (GRCm39) |
D250G |
possibly damaging |
Het |
| Jsrp1 |
T |
G |
10: 80,646,349 (GRCm39) |
M70L |
probably benign |
Het |
| Kcmf1 |
G |
T |
6: 72,827,470 (GRCm39) |
|
probably null |
Het |
| Med23 |
T |
C |
10: 24,788,715 (GRCm39) |
V1368A |
probably benign |
Het |
| Myl3 |
A |
C |
9: 110,596,997 (GRCm39) |
D119A |
probably damaging |
Het |
| Ncoa6 |
TGC |
TGCGC |
2: 155,250,211 (GRCm39) |
|
probably null |
Het |
| Nos1 |
G |
T |
5: 118,031,943 (GRCm39) |
C297F |
probably damaging |
Het |
| Oas1d |
G |
A |
5: 121,054,955 (GRCm39) |
A176T |
possibly damaging |
Het |
| Odf2l |
A |
T |
3: 144,830,084 (GRCm39) |
I19F |
possibly damaging |
Het |
| Or6c1b |
T |
C |
10: 129,273,140 (GRCm39) |
I153T |
possibly damaging |
Het |
| Or6c209 |
G |
A |
10: 129,483,522 (GRCm39) |
C175Y |
probably benign |
Het |
| Pfkfb2 |
A |
T |
1: 130,642,279 (GRCm39) |
S5R |
probably benign |
Het |
| Pign |
G |
T |
1: 105,480,130 (GRCm39) |
A848E |
probably damaging |
Het |
| Pomgnt2 |
A |
T |
9: 121,811,326 (GRCm39) |
V485E |
probably damaging |
Het |
| Ryr2 |
T |
A |
13: 11,583,361 (GRCm39) |
K4764N |
probably damaging |
Het |
| Scgb1b19 |
A |
G |
7: 32,987,067 (GRCm39) |
T73A |
probably damaging |
Het |
| Slc35d3 |
T |
C |
10: 19,724,944 (GRCm39) |
E304G |
probably damaging |
Het |
| Snta1 |
A |
G |
2: 154,225,757 (GRCm39) |
V209A |
probably benign |
Het |
| Spdye4b |
A |
T |
5: 143,181,430 (GRCm39) |
D95V |
probably damaging |
Het |
| Srek1 |
T |
C |
13: 103,880,194 (GRCm39) |
T455A |
unknown |
Het |
| Tie1 |
T |
A |
4: 118,341,550 (GRCm39) |
E254V |
probably damaging |
Het |
| Tigd4 |
A |
G |
3: 84,501,452 (GRCm39) |
H123R |
probably benign |
Het |
| Tmem144 |
G |
A |
3: 79,746,580 (GRCm39) |
|
probably benign |
Het |
| Trim60 |
C |
T |
8: 65,453,251 (GRCm39) |
A333T |
probably damaging |
Het |
| Vmn2r82 |
A |
T |
10: 79,232,339 (GRCm39) |
R779S |
probably benign |
Het |
| Wdr91 |
T |
C |
6: 34,883,620 (GRCm39) |
R132G |
possibly damaging |
Het |
| Zfp445 |
A |
G |
9: 122,681,421 (GRCm39) |
V840A |
probably damaging |
Het |
|
| Other mutations in D2hgdh |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL02173:D2hgdh
|
APN |
1 |
93,757,611 (GRCm39) |
missense |
probably benign |
0.06 |
|
IGL02506:D2hgdh
|
APN |
1 |
93,757,507 (GRCm39) |
missense |
probably damaging |
0.98 |
|
IGL02995:D2hgdh
|
APN |
1 |
93,757,558 (GRCm39) |
missense |
probably damaging |
1.00 |
|
PIT1430001:D2hgdh
|
UTSW |
1 |
93,754,001 (GRCm39) |
unclassified |
probably benign |
|
|
PIT4418001:D2hgdh
|
UTSW |
1 |
93,766,590 (GRCm39) |
missense |
possibly damaging |
0.90 |
|
R0069:D2hgdh
|
UTSW |
1 |
93,763,009 (GRCm39) |
missense |
possibly damaging |
0.93 |
|
R0538:D2hgdh
|
UTSW |
1 |
93,754,099 (GRCm39) |
missense |
probably damaging |
0.97 |
|
R2267:D2hgdh
|
UTSW |
1 |
93,763,157 (GRCm39) |
missense |
probably damaging |
0.97 |
|
R2268:D2hgdh
|
UTSW |
1 |
93,763,157 (GRCm39) |
missense |
probably damaging |
0.97 |
|
R2269:D2hgdh
|
UTSW |
1 |
93,763,157 (GRCm39) |
missense |
probably damaging |
0.97 |
|
R4419:D2hgdh
|
UTSW |
1 |
93,757,535 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5322:D2hgdh
|
UTSW |
1 |
93,757,620 (GRCm39) |
critical splice donor site |
probably null |
|
|
R6018:D2hgdh
|
UTSW |
1 |
93,754,182 (GRCm39) |
missense |
probably benign |
0.03 |
|
R6264:D2hgdh
|
UTSW |
1 |
93,754,177 (GRCm39) |
missense |
probably damaging |
0.97 |
|
R6750:D2hgdh
|
UTSW |
1 |
93,754,129 (GRCm39) |
missense |
probably benign |
0.01 |
|
R6814:D2hgdh
|
UTSW |
1 |
93,763,025 (GRCm39) |
missense |
possibly damaging |
0.94 |
|
R7058:D2hgdh
|
UTSW |
1 |
93,763,096 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7473:D2hgdh
|
UTSW |
1 |
93,765,800 (GRCm39) |
missense |
probably damaging |
0.96 |
|
R7683:D2hgdh
|
UTSW |
1 |
93,766,687 (GRCm39) |
critical splice donor site |
probably null |
|
|
R9151:D2hgdh
|
UTSW |
1 |
93,754,338 (GRCm39) |
missense |
probably benign |
0.08 |
|
| Predicted Primers |
PCR Primer
(F):5'- CCCTCTCAAGAGCAGGAACAATGG -3'
(R):5'- GCTCACTTTAGCCAAGTGCTACACC -3'
Sequencing Primer
(F):5'- AGGAACAATGGTGCTCCCTC -3'
(R):5'- GCCGATTTTATTCTCAGAAGACC -3'
|
| Posted On |
2013-04-11 |
Incidental Mutation