Mutagenetix > Incidental Mutation

Incidental Mutation 'R2269:D2hgdh'

242281

Institutional Source

Beutler Lab

Gene Symbol

D2hgdh

Ensembl Gene

ENSMUSG00000073609

Gene Name

D-2-hydroxyglutarate dehydrogenase

Synonyms

MMRRC Submission

040269-MU

Accession Numbers

Essential gene?

Possibly non essential (E-score: 0.266) question?

Stock #

R2269 (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: 99.2%
3x: 98.7%
10x: 97.5%
20x: 95.7%

Validation Efficiency

98% (79/81)

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: 77 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abca16	A	G	7: 120,030,383 (GRCm39)	D165G	probably benign	Het
Abca8a	A	C	11: 109,917,718 (GRCm39)	F1574V	probably damaging	Het
Adh6a	A	T	3: 138,034,857 (GRCm39)	I329L	probably benign	Het
Agap2	T	A	10: 126,918,297 (GRCm39)		probably benign	Het
Ager	A	T	17: 34,818,124 (GRCm39)	I185F	probably damaging	Het
Agrn	C	T	4: 156,263,675 (GRCm39)	G173R	probably damaging	Het
Arhgef16	T	A	4: 154,369,490 (GRCm39)	H329L	probably damaging	Het
Astn1	T	C	1: 158,329,669 (GRCm39)	Y175H	probably damaging	Het
Banp	A	G	8: 122,702,662 (GRCm39)	T70A	probably benign	Het
Bcl11b	T	C	12: 107,881,910 (GRCm39)	T802A	possibly damaging	Het
Ces2a	A	T	8: 105,466,822 (GRCm39)	I65F	probably benign	Het
Cflar	G	A	1: 58,780,206 (GRCm39)		probably null	Het
Clec16a	G	A	16: 10,462,650 (GRCm39)	R656H	probably damaging	Het
Cntn1	A	G	15: 92,192,863 (GRCm39)		probably benign	Het
Coasy	A	G	11: 100,976,708 (GRCm39)	T493A	probably benign	Het
Col16a1	C	A	4: 129,946,711 (GRCm39)	H111Q	probably benign	Het
Commd8	A	G	5: 72,322,765 (GRCm39)	W51R	probably damaging	Het
Cyp3a41b	A	T	5: 145,514,976 (GRCm39)	V83D	probably benign	Het
Dcun1d4	T	A	5: 73,638,618 (GRCm39)		probably benign	Het
Decr2	C	A	17: 26,302,858 (GRCm39)	V173L	probably benign	Het
Defb11	A	G	8: 22,395,444 (GRCm39)	*78Q	probably null	Het
Dock3	C	A	9: 106,818,525 (GRCm39)	V1190F	probably damaging	Het
Dusp1	A	T	17: 26,726,093 (GRCm39)	I200N	probably damaging	Het
Efna1	G	A	3: 89,183,646 (GRCm39)	A60V	possibly damaging	Het
Egfl8	C	T	17: 34,832,832 (GRCm39)	V253M	probably damaging	Het
Epb41	T	A	4: 131,691,458 (GRCm39)	N623I	probably benign	Het
Fbxw22	C	T	9: 109,213,062 (GRCm39)	R295K	probably benign	Het
Foxn4	T	C	5: 114,393,662 (GRCm39)	T486A	probably damaging	Het
Gbe1	C	T	16: 70,233,840 (GRCm39)	A239V	probably damaging	Het
Gpatch3	C	T	4: 133,311,118 (GRCm39)	A518V	possibly damaging	Het
Gpc6	A	T	14: 118,125,932 (GRCm39)		probably null	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
Hnrnpul1	A	G	7: 25,450,299 (GRCm39)	Y138H	probably damaging	Het
Itgal	A	G	7: 126,905,873 (GRCm39)	I352V	possibly damaging	Het
Klhl31	A	G	9: 77,557,440 (GRCm39)	D52G	possibly damaging	Het
Klk1b21	T	C	7: 43,753,863 (GRCm39)	I49T	possibly damaging	Het
Lama2	T	A	10: 26,868,932 (GRCm39)	I2838F	probably damaging	Het
Lrrc43	A	T	5: 123,641,354 (GRCm39)	T513S	probably damaging	Het
Lsmem1	GTACATACATACATACATACATACATACA	GTACATACATACATACATACATACATACATACA	12: 40,235,260 (GRCm39)		probably null	Het
Mamdc2	A	T	19: 23,281,267 (GRCm39)		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
Mroh5	T	C	15: 73,664,997 (GRCm39)	N258D	probably benign	Het
Mrpl28	T	C	17: 26,345,285 (GRCm39)	V235A	probably benign	Het
Mtbp	G	A	15: 55,432,556 (GRCm39)		probably null	Het
Mtss2	A	G	8: 111,455,362 (GRCm39)	K92E	possibly damaging	Het
Muc4	C	A	16: 32,754,529 (GRCm38)	H1468N	probably benign	Het
Nav1	A	T	1: 135,399,974 (GRCm39)	L532*	probably null	Het
Or10ak16	A	T	4: 118,751,071 (GRCm39)	R264W	probably damaging	Het
Or1e23	A	G	11: 73,407,309 (GRCm39)	S239P	probably damaging	Het
Or51f1d	G	A	7: 102,701,344 (GRCm39)	V280I	probably benign	Het
Pappa2	A	G	1: 158,684,841 (GRCm39)	M766T	probably damaging	Het
Pkhd1	C	T	1: 20,604,759 (GRCm39)		probably null	Het
Plch2	T	C	4: 155,077,461 (GRCm39)	E423G	probably benign	Het
Prrc1	G	T	18: 57,514,718 (GRCm39)	D312Y	probably damaging	Het
Pxdn	T	A	12: 30,055,774 (GRCm39)	V1220E	probably damaging	Het
Robo1	T	A	16: 72,775,660 (GRCm39)	F728L	probably benign	Het
Rtel1	G	T	2: 180,977,796 (GRCm39)	Q292H	probably benign	Het
Sh3bp4	G	A	1: 89,073,314 (GRCm39)	V721I	possibly damaging	Het
Slc2a10	T	A	2: 165,356,701 (GRCm39)	C120*	probably null	Het
Srd5a2	T	C	17: 74,331,485 (GRCm39)	R171G	probably damaging	Het
Srsf4	T	C	4: 131,624,993 (GRCm39)	V130A	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
Tbx1	T	C	16: 18,400,744 (GRCm39)		probably null	Het
Tmem233	G	C	5: 116,189,517 (GRCm39)		probably benign	Het
Tmem252	T	C	19: 24,651,455 (GRCm39)	I8T	probably benign	Het
Vcp	G	A	4: 42,980,833 (GRCm39)	A759V	possibly damaging	Het
Vmn2r107	T	C	17: 20,595,817 (GRCm39)	I790T	possibly damaging	Het
Vmn2r77	T	C	7: 86,460,897 (GRCm39)	V741A	probably benign	Het
Vps13c	T	C	9: 67,828,229 (GRCm39)	V1461A	possibly damaging	Het
Ylpm1	T	A	12: 85,061,824 (GRCm39)	V575E	unknown	Het
Zbp1	T	A	2: 173,060,616 (GRCm39)		probably benign	Het
Zfp280d	C	A	9: 72,209,052 (GRCm39)		probably benign	Het
Zkscan5	A	G	5: 145,142,277 (GRCm39)	Y58C	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
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
R2268: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'- GGGTCAGCATTTCCAGAGAAGG -3'
(R):5'- TTCAGGCTACACTCTGGACAC -3'

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

Posted On

2014-10-16