Mutagenetix > Incidental Mutation

Incidental Mutation 'R2268:D2hgdh'

242194

Institutional Source

Beutler Lab

Gene Symbol

D2hgdh

Ensembl Gene

ENSMUSG00000073609

Gene Name

D-2-hydroxyglutarate dehydrogenase

Synonyms

MMRRC Submission

040268-MU

Accession Numbers

Essential gene?

Possibly non essential (E-score: 0.273) question?

Stock #

R2268 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

93752631-93780070 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

C to T at 93763157 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Alanine to Valine at position 314 (A314V)

Ref Sequence

ENSEMBL: ENSMUSP00000108502 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000097633] [ENSMUST00000112881] [ENSMUST00000188532] [ENSMUST00000189154]

AlphaFold

Q8CIM3

Predicted Effect

probably damaging
Transcript: ENSMUST00000097633
AA Change: A292V

PolyPhen 2 Score 0.968 (Sensitivity: 0.77; Specificity: 0.95)

SMART Domains

Protein: ENSMUSP00000095235
Gene: ENSMUSG00000073609
AA Change: A292V

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 damaging
Transcript: ENSMUST00000112881
AA Change: A314V

PolyPhen 2 Score 0.968 (Sensitivity: 0.77; Specificity: 0.95)

SMART Domains

Protein: ENSMUSP00000108502
Gene: ENSMUSG00000073609
AA Change: A314V

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

probably benign
Transcript: ENSMUST00000186783

Predicted Effect

probably benign
Transcript: ENSMUST00000188532

Predicted Effect

probably benign
Transcript: ENSMUST00000189154

SMART Domains

Protein: ENSMUSP00000140506
Gene: ENSMUSG00000073609

Domain	Start	End	E-Value	Type
Pfam:FAD_binding_4	114	179	3.2e-10	PFAM

Meta Mutation Damage Score

0.1723

Coding Region Coverage

1x: 99.1%
3x: 98.5%
10x: 97.2%
20x: 94.7%

Validation Efficiency

100% (82/82)

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: 82 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Acox2	A	T	14: 8,253,496 (GRCm38)	M217K	probably damaging	Het
Adam34	C	T	8: 44,103,647 (GRCm39)	R666H	probably benign	Het
Adap2	G	T	11: 80,056,552 (GRCm39)	Q188H	probably damaging	Het
Adgrb3	T	C	1: 25,150,898 (GRCm39)	T872A	possibly damaging	Het
Ahnak	A	G	19: 8,987,938 (GRCm39)	K3074R	possibly damaging	Het
Ano7	A	T	1: 93,308,161 (GRCm39)	D64V	possibly damaging	Het
Apob	T	C	12: 8,065,475 (GRCm39)	F4115S	possibly damaging	Het
Arl13a	A	G	X: 133,106,162 (GRCm39)	Q236R	possibly damaging	Het
Astn1	T	C	1: 158,329,669 (GRCm39)	Y175H	probably damaging	Het
Atn1	C	G	6: 124,723,203 (GRCm39)		probably benign	Het
Ccser1	C	T	6: 61,547,827 (GRCm39)	T118M	probably damaging	Het
Cenpe	A	G	3: 134,967,397 (GRCm39)	T2180A	probably benign	Het
Col17a1	G	A	19: 47,638,550 (GRCm39)	P1173S	probably benign	Het
Commd8	A	G	5: 72,322,765 (GRCm39)	W51R	probably damaging	Het
Cyp4f17	G	T	17: 32,736,928 (GRCm39)	V87F	probably benign	Het
Dcun1d4	T	A	5: 73,638,618 (GRCm39)		probably benign	Het
Dhodh	A	G	8: 110,321,306 (GRCm39)	F360S	possibly damaging	Het
Dipk2b	A	G	X: 18,289,926 (GRCm39)	S179P	possibly damaging	Het
Dynap	C	T	18: 70,374,218 (GRCm39)	A103T	probably benign	Het
Edem2	G	A	2: 155,544,137 (GRCm39)	P538S	probably benign	Het
Egfl8	C	T	17: 34,832,832 (GRCm39)	V253M	probably damaging	Het
Erich6	A	T	3: 58,526,260 (GRCm39)	S581T	probably benign	Het
Fam117b	T	C	1: 59,952,789 (GRCm39)	L156P	probably damaging	Het
Fbn1	G	T	2: 125,163,661 (GRCm39)	A2065E	possibly damaging	Het
Foxn4	T	C	5: 114,393,662 (GRCm39)	T486A	probably damaging	Het
Fzd9	A	G	5: 135,279,148 (GRCm39)	S246P	probably damaging	Het
Hdhd2	C	T	18: 77,052,866 (GRCm39)	T172M	probably benign	Het
Heatr5a	T	C	12: 51,940,528 (GRCm39)	D1444G	possibly damaging	Het
Hmcn1	A	G	1: 150,500,349 (GRCm39)		probably benign	Het
Hps3	G	A	3: 20,067,099 (GRCm39)		probably benign	Het
Hr	A	T	14: 70,795,547 (GRCm39)	D393V	probably benign	Het
Ido2	T	C	8: 25,025,268 (GRCm39)	Y253C	probably damaging	Het
Irs2	T	C	8: 11,057,586 (GRCm39)	E282G	probably damaging	Het
Itih4	A	G	14: 30,614,385 (GRCm39)	D445G	probably damaging	Het
Kif14	T	A	1: 136,447,486 (GRCm39)	C1430*	probably null	Het
Kir3dl1	A	G	X: 135,425,784 (GRCm39)	R53G	probably benign	Het
Lama2	T	A	10: 26,868,932 (GRCm39)	I2838F	probably damaging	Het
Lamb1	A	T	12: 31,377,644 (GRCm39)	I1630F	probably damaging	Het
Lsmem1	GTACATACATACATACATACATACATACA	GTACATACATACATACATACATACATACATACA	12: 40,235,260 (GRCm39)		probably null	Het
Magi3	G	A	3: 103,928,382 (GRCm39)		probably benign	Het
Mink1	G	A	11: 70,492,550 (GRCm39)		probably null	Het
Mmrn2	A	G	14: 34,121,449 (GRCm39)	K773R	probably benign	Het
Mpdz	A	G	4: 81,301,628 (GRCm39)	S266P	probably damaging	Het
Mrc2	G	A	11: 105,239,257 (GRCm39)		probably null	Het
Mtbp	G	A	15: 55,432,556 (GRCm39)		probably null	Het
Mybphl	A	G	3: 108,272,317 (GRCm39)	E2G	probably damaging	Het
Myoc	C	T	1: 162,476,625 (GRCm39)	T443M	probably damaging	Het
Nav1	A	T	1: 135,399,974 (GRCm39)	L532*	probably null	Het
Nbeal1	T	A	1: 60,370,037 (GRCm39)		probably benign	Het
Nfix	CAAAAA	CAAAA	8: 85,442,876 (GRCm39)		probably null	Het
Opcml	T	C	9: 28,814,651 (GRCm39)	I301T	possibly damaging	Het
Or10ak16	A	T	4: 118,751,071 (GRCm39)	R264W	probably damaging	Het
Or8b1	T	A	9: 38,399,504 (GRCm39)	Y60N	probably damaging	Het
Pappa2	A	G	1: 158,684,841 (GRCm39)	M766T	probably damaging	Het
Phf8	T	C	X: 150,355,597 (GRCm39)	L520S	possibly damaging	Het
Phka1	A	G	X: 101,584,716 (GRCm39)		probably benign	Het
Ppp2ca	G	A	11: 52,008,913 (GRCm39)	G138R	probably damaging	Het
Prrc1	G	T	18: 57,514,718 (GRCm39)	D312Y	probably damaging	Het
Rdh7	A	G	10: 127,720,530 (GRCm39)	S281P	probably benign	Het
Rps17	C	T	7: 80,994,746 (GRCm39)	R5H	probably benign	Het
Scgb1b2	T	A	7: 30,991,201 (GRCm39)		probably benign	Het
Skic3	T	G	13: 76,260,393 (GRCm39)		probably benign	Het
Slc35a3	T	C	3: 116,467,285 (GRCm39)	K325E	possibly damaging	Het
Snap23	A	G	2: 120,429,793 (GRCm39)	T213A	probably benign	Het
Spag17	C	A	3: 99,969,182 (GRCm39)		probably null	Het
Srebf1	A	G	11: 60,097,973 (GRCm39)	S44P	probably damaging	Het
St8sia5	T	C	18: 77,320,526 (GRCm39)	S93P	probably damaging	Het
Styk1	T	C	6: 131,289,539 (GRCm39)	E25G	probably benign	Het
Taar8b	T	C	10: 23,967,270 (GRCm39)	N308S	probably damaging	Het
Tbc1d14	A	G	5: 36,700,561 (GRCm39)	L269P	possibly damaging	Het
Tbc1d22b	A	G	17: 29,818,828 (GRCm39)	H394R	probably damaging	Het
Tbx5	A	T	5: 119,983,174 (GRCm39)		probably null	Het
Tgfbr3l	A	G	8: 4,300,506 (GRCm39)	E228G	probably benign	Het
Tlr5	T	A	1: 182,802,600 (GRCm39)	S635T	possibly damaging	Het
Tmem233	G	C	5: 116,189,517 (GRCm39)		probably benign	Het
Tymp	A	T	15: 89,258,011 (GRCm39)	V378D	probably damaging	Het
Vangl1	A	T	3: 102,104,160 (GRCm39)	Y7N	probably damaging	Het
Vav2	A	T	2: 27,182,667 (GRCm39)		probably null	Het
Vcp	G	A	4: 42,980,833 (GRCm39)	A759V	possibly damaging	Het
Vmn2r15	A	G	5: 109,441,073 (GRCm39)	Y262H	probably benign	Het
Vmn2r76	T	C	7: 85,879,707 (GRCm39)	M198V	probably benign	Het
Zfp831	A	C	2: 174,486,034 (GRCm39)	R236S	probably benign	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
R0080:D2hgdh	UTSW	1	93,754,177 (GRCm39)	missense	probably damaging	0.97
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
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'- GTTGGGTCAGCATTTCCAGAG -3'
(R):5'- AGGCTACACTCTGGACACCTAG -3'

Sequencing Primer
(F):5'- GTGTAGGAAGGCCCATCTCTTTC -3'
(R):5'- TACACTCTGGACACCTAGAGGGC -3'

Posted On

2014-10-16