Mutagenetix > Incidental Mutation

Incidental Mutation 'R6264:D2hgdh'

506861

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 #

R6264 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

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: 99.9%
3x: 99.7%
10x: 98.5%
20x: 96.1%

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: 60 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abcc3	A	G	11: 94,264,824 (GRCm39)	Y175H	probably damaging	Het
Agtpbp1	A	T	13: 59,598,114 (GRCm39)	V1165D	possibly damaging	Het
Ahsg	A	G	16: 22,717,611 (GRCm39)	D224G	probably benign	Het
Akap11	T	C	14: 78,749,861 (GRCm39)	D842G	possibly damaging	Het
Anln	T	C	9: 22,245,413 (GRCm39)	N186D	possibly damaging	Het
Aqr	A	G	2: 113,940,445 (GRCm39)	Y1234H	probably damaging	Het
Ccdc162	A	G	10: 41,570,464 (GRCm39)	F7S	probably benign	Het
Cltc	T	C	11: 86,596,084 (GRCm39)	Y1222C	probably damaging	Het
Coro2a	C	T	4: 46,562,912 (GRCm39)	V81I	probably damaging	Het
Cpa5	T	C	6: 30,613,984 (GRCm39)	V42A	probably damaging	Het
Ddx6	A	G	9: 44,540,049 (GRCm39)	N326D	probably damaging	Het
Dedd2	A	G	7: 24,903,215 (GRCm39)	L248P	possibly damaging	Het
Frem3	T	A	8: 81,341,832 (GRCm39)	I1375N	probably damaging	Het
Gm12185	T	C	11: 48,807,002 (GRCm39)	N63S	probably benign	Het
H2-Aa	A	G	17: 34,502,172 (GRCm39)	S250P	probably damaging	Het
Hbs1l	T	C	10: 21,243,656 (GRCm39)	S667P	possibly damaging	Het
Hc	T	A	2: 34,896,285 (GRCm39)		probably null	Het
Hoxd4	A	T	2: 74,557,729 (GRCm39)	Y36F	possibly damaging	Het
Ifi207	A	G	1: 173,555,111 (GRCm39)	V864A	probably damaging	Het
Igsf10	T	A	3: 59,235,928 (GRCm39)	T1418S	possibly damaging	Het
Klhl41	T	C	2: 69,510,176 (GRCm39)		probably null	Het
Lman2l	T	C	1: 36,477,850 (GRCm39)	N162S	probably damaging	Het
Lrr1	T	G	12: 69,215,655 (GRCm39)	V9G	probably damaging	Het
Marchf5	T	C	19: 37,198,140 (GRCm39)	I127T	probably damaging	Het
Med12l	T	C	3: 59,163,423 (GRCm39)	L1350P	probably damaging	Het
Mmp25	G	A	17: 23,849,768 (GRCm39)	A541V	possibly damaging	Het
Myh10	T	A	11: 68,636,241 (GRCm39)	I210N	probably benign	Het
Myo5c	A	G	9: 75,182,836 (GRCm39)	N825S	probably benign	Het
Nav3	T	C	10: 109,524,694 (GRCm39)	T2312A	probably damaging	Het
Ndrg4	G	T	8: 96,436,396 (GRCm39)	R208L	probably damaging	Het
Nell2	G	A	15: 95,244,706 (GRCm39)	P464S	probably damaging	Het
Nrxn3	T	A	12: 90,299,011 (GRCm39)	Y374N	probably damaging	Het
Oprd1	A	C	4: 131,841,365 (GRCm39)	C198G	possibly damaging	Het
Pik3ca	T	C	3: 32,494,863 (GRCm39)		probably null	Het
Plin4	T	G	17: 56,411,787 (GRCm39)	D748A	possibly damaging	Het
Pramel23	T	G	4: 143,425,722 (GRCm39)	T74P	possibly damaging	Het
Prkg2	T	G	5: 99,082,223 (GRCm39)	K52Q	probably benign	Het
Ptprk	A	T	10: 28,442,669 (GRCm39)	E890D	probably damaging	Het
Rab27b	T	C	18: 70,122,659 (GRCm39)	D100G	probably damaging	Het
Ranbp6	T	C	19: 29,790,026 (GRCm39)	T109A	probably benign	Het
Rarb	T	A	14: 16,818,819 (GRCm38)	M17L	probably benign	Het
Rasgrf2	T	C	13: 92,167,293 (GRCm39)	H260R	probably damaging	Het
Rec8	T	A	14: 55,856,636 (GRCm39)	D109E	probably damaging	Het
Scd4	C	A	19: 44,327,398 (GRCm39)	S158*	probably null	Het
Scn7a	T	A	2: 66,505,870 (GRCm39)	E1673V	possibly damaging	Het
Sit1	A	T	4: 43,482,651 (GRCm39)	D169E	possibly damaging	Het
Slc16a14	G	T	1: 84,885,130 (GRCm39)	Q470K	probably benign	Het
Slc43a2	T	A	11: 75,457,900 (GRCm39)	C392S	possibly damaging	Het
Smg1	A	G	7: 117,765,310 (GRCm39)		probably benign	Het
Sstr2	A	T	11: 113,515,932 (GRCm39)	I284F	probably damaging	Het
Tep1	C	T	14: 51,082,970 (GRCm39)	V1013M	probably damaging	Het
Tmem120b	T	G	5: 123,253,763 (GRCm39)	L232R	probably damaging	Het
Tmem9b	C	A	7: 109,344,612 (GRCm39)	V75F	probably damaging	Het
Trappc3	A	G	4: 126,167,731 (GRCm39)	S97G	probably damaging	Het
Ube3c	T	C	5: 29,795,829 (GRCm39)	F73L	probably damaging	Het
Vmn1r127	C	A	7: 21,052,930 (GRCm39)	C286F	probably benign	Het
Vmn1r44	T	C	6: 89,870,652 (GRCm39)	S133P	probably benign	Het
Vps8	C	T	16: 21,378,099 (GRCm39)	Q635*	probably null	Het
Vwa8	A	G	14: 79,324,252 (GRCm39)	E1185G	possibly damaging	Het
Zfp354c	G	A	11: 50,706,274 (GRCm39)	T267I	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
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
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'- TGCTTCATTGCTTACGAATCG -3'
(R):5'- CTTCAGCCAGTCAACGTTGC -3'

Sequencing Primer
(F):5'- GCTTACGAATCGCAAATTCAATCTC -3'
(R):5'- AGCCAGTCAACGTTGCATGTC -3'

Posted On

2018-03-15