Mutagenetix > Incidental Mutation

Incidental Mutation 'PIT4418001:D2hgdh'

555552

Institutional Source

Beutler Lab

Gene Symbol

D2hgdh

Ensembl Gene

ENSMUSG00000073609

Gene Name

D-2-hydroxyglutarate dehydrogenase

Synonyms

Accession Numbers

Essential gene?

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

Stock #

PIT4418001 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

93752631-93780070 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

C to T at 93766590 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Histidine to Tyrosine at position 385 (H385Y)

Ref Sequence

ENSEMBL: ENSMUSP00000108502 (fasta)

Gene Model

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

AlphaFold

Q8CIM3

Predicted Effect

possibly damaging
Transcript: ENSMUST00000097633
AA Change: H363Y

PolyPhen 2 Score 0.896 (Sensitivity: 0.82; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000095235
Gene: ENSMUSG00000073609
AA Change: H363Y

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

possibly damaging
Transcript: ENSMUST00000112881
AA Change: H385Y

PolyPhen 2 Score 0.896 (Sensitivity: 0.82; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000108502
Gene: ENSMUSG00000073609
AA Change: H385Y

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 damaging
Transcript: ENSMUST00000188532
AA Change: H50Y

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)

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

Coding Region Coverage

1x: 93.3%
3x: 90.8%
10x: 84.7%
20x: 71.4%

Validation Efficiency

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: 68 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abtb1	T	C	6: 88,816,630 (GRCm39)	Y100C	possibly damaging	Het
Adamtsl1	T	C	4: 86,161,961 (GRCm39)	Y365H	probably damaging	Het
Atad2b	A	T	12: 5,074,587 (GRCm39)	I1049F	probably benign	Het
Atg9b	A	T	5: 24,590,513 (GRCm39)	S859T	possibly damaging	Het
Banp	G	A	8: 122,732,365 (GRCm39)	A380T	probably damaging	Het
Brinp3	C	T	1: 146,777,161 (GRCm39)	T536I	probably damaging	Het
Cacna1c	T	C	6: 118,631,384 (GRCm39)	E1155G		Het
Capn12	T	C	7: 28,585,961 (GRCm39)	S270P	probably benign	Het
Cbs	A	T	17: 31,834,495 (GRCm39)	I498N	possibly damaging	Het
Cep68	T	C	11: 20,189,731 (GRCm39)	K427R	probably benign	Het
Cobl	G	A	11: 12,206,240 (GRCm39)	T545I	possibly damaging	Het
Cr2	T	A	1: 194,839,760 (GRCm39)	M556L	probably benign	Het
Crebbp	A	G	16: 3,932,689 (GRCm39)	S1068P	probably benign	Het
Dennd1b	T	C	1: 139,008,999 (GRCm39)	L159P		Het
Dnajb4	A	T	3: 151,899,134 (GRCm39)	F31I	possibly damaging	Het
Dnajc16	A	G	4: 141,498,260 (GRCm39)	F369S	probably damaging	Het
Dtl	A	T	1: 191,273,429 (GRCm39)	L493H	possibly damaging	Het
Efcab5	T	A	11: 77,022,877 (GRCm39)	Q612L	possibly damaging	Het
Efr3b	A	T	12: 4,030,490 (GRCm39)	L407Q	possibly damaging	Het
Ehbp1	T	A	11: 22,003,494 (GRCm39)	Q1085L	probably damaging	Het
Ell	T	C	8: 71,034,331 (GRCm39)	V199A	probably damaging	Het
Elmod2	G	T	8: 84,048,171 (GRCm39)	T97K	probably benign	Het
Epn3	T	C	11: 94,386,956 (GRCm39)	E138G	probably damaging	Het
Esf1	A	T	2: 140,001,697 (GRCm39)	F383L	probably benign	Het
Fam193a	A	T	5: 34,597,879 (GRCm39)	T559S	probably damaging	Het
Galr2	T	C	11: 116,174,084 (GRCm39)	V238A	probably benign	Het
Gm3476	T	C	14: 6,118,411 (GRCm38)	I237M	probably benign	Het
Gm5160	A	T	18: 14,558,339 (GRCm39)	I139F	probably damaging	Het
Gpr15	T	C	16: 58,538,313 (GRCm39)	T259A	probably benign	Het
Iffo1	A	G	6: 125,126,746 (GRCm39)	K293E	possibly damaging	Het
Ikbip	T	A	10: 90,932,395 (GRCm39)	H346Q	probably benign	Het
Il4ra	G	A	7: 125,175,510 (GRCm39)	G573S	probably benign	Het
Ing2	A	T	8: 48,122,125 (GRCm39)	M141K	probably benign	Het
Itga6	T	C	2: 71,664,414 (GRCm39)	S517P	probably benign	Het
Itprid1	T	G	6: 55,945,330 (GRCm39)	S684A	probably damaging	Het
Kcnab1	A	G	3: 65,265,741 (GRCm39)	E295G	probably benign	Het
Klhl21	A	C	4: 152,099,835 (GRCm39)	Y515S	possibly damaging	Het
Lcn9	A	T	2: 25,714,553 (GRCm39)	Y139F	probably damaging	Het
Mcemp1	G	T	8: 3,717,052 (GRCm39)	L64F	probably null	Het
Mos	T	C	4: 3,870,814 (GRCm39)	D334G	possibly damaging	Het
Myo9b	T	G	8: 71,775,591 (GRCm39)	F338V	probably damaging	Het
Nefl	G	A	14: 68,323,979 (GRCm39)	V406M	probably damaging	Het
Nfam1	C	A	15: 82,885,689 (GRCm39)	R181L	probably damaging	Het
Ntn5	A	G	7: 45,335,925 (GRCm39)	R119G	probably damaging	Het
Or12e10	G	T	2: 87,640,938 (GRCm39)	C258F	probably damaging	Het
Or5b101	A	T	19: 13,005,095 (GRCm39)	Y199*	probably null	Het
Or7a40	T	C	16: 16,491,719 (GRCm39)	N42S	probably damaging	Het
Plch2	A	T	4: 155,073,960 (GRCm39)	V914E	probably damaging	Het
Ppp1r12c	T	C	7: 4,504,266 (GRCm39)	Q111R	probably null	Het
Ptchd3	T	A	11: 121,732,566 (GRCm39)	Y485*	probably null	Het
Ptchd4	T	A	17: 42,813,980 (GRCm39)	I627N	probably damaging	Het
Retnlb	T	C	16: 48,637,631 (GRCm39)	V19A	probably benign	Het
Rimbp2	T	A	5: 128,857,425 (GRCm39)	T809S	probably benign	Het
Sema6c	T	A	3: 95,077,401 (GRCm39)	D404E	possibly damaging	Het
Slc22a16	C	T	10: 40,479,821 (GRCm39)	A631V	unknown	Het
Snai3	A	T	8: 123,183,073 (GRCm39)	H157Q	probably benign	Het
Snx15	T	C	19: 6,173,961 (GRCm39)	Y52C	probably damaging	Het
Strbp	T	C	2: 37,535,504 (GRCm39)	E68G	probably benign	Het
Sun1	T	A	5: 139,212,343 (GRCm39)	D155E	probably damaging	Het
Susd2	T	C	10: 75,474,183 (GRCm39)	D627G	probably benign	Het
Tas2r108	T	A	6: 40,470,614 (GRCm39)	I30K	probably damaging	Het
Tmc2	T	C	2: 130,090,571 (GRCm39)	V639A	probably damaging	Het
Trmt1	T	C	8: 85,424,299 (GRCm39)	Y445H	probably damaging	Het
Ttn	A	T	2: 76,597,554 (GRCm39)	N19786K	probably damaging	Het
Vmn1r79	T	G	7: 11,910,766 (GRCm39)	V216G	probably damaging	Het
Wdr64	C	A	1: 175,571,160 (GRCm39)	Y331*	probably null	Het
Zfyve28	A	T	5: 34,390,721 (GRCm39)	V180E	probably damaging	Het
Zic4	C	T	9: 91,261,447 (GRCm39)	T234I	possibly 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
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
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'- CCCATGTGAAATTTAGCGAGC -3'
(R):5'- GAGGTGTCTTGGCCATCTAC -3'

Sequencing Primer
(F):5'- TAGCGAGCCTGAATGCTTC -3'
(R):5'- TACCCCATCTCTGCAGGAC -3'

Posted On

2019-06-07