Mutagenetix > Incidental Mutation

Incidental Mutation 'R6875:Ogdh'

536386

Institutional Source

Beutler Lab

Gene Symbol

Ogdh

Ensembl Gene

ENSMUSG00000020456

Gene Name

oxoglutarate (alpha-ketoglutarate) dehydrogenase (lipoamide)

Synonyms

2210403E04Rik, alpha-ketoglutarate dehydrogenase, d1401, 2210412K19Rik

MMRRC Submission

Accession Numbers

Genbank: NM_010956; MGI: 1098267; Ensembl: ENSMUST00000093350

Is this an essential gene?

Essential (E-score: 1.000) question?

Stock #

R6875 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

6291633-6356642 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 6340477 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Tyrosine to Cysteine at position 365 (Y365C)

Ref Sequence

ENSEMBL: ENSMUSP00000091041 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000003461] [ENSMUST00000081894] [ENSMUST00000093350] [ENSMUST00000101554]

AlphaFold

Q60597

PDB Structure

Structure of the m67 high-affinity mutant of the 2C TCR in complex with Ld/QL9 [X-RAY DIFFRACTION]
42F3 QL9/H2-Ld complex [X-RAY DIFFRACTION]

Predicted Effect

probably benign
Transcript: ENSMUST00000003461
AA Change: Y354C

PolyPhen 2 Score 0.072 (Sensitivity: 0.94; Specificity: 0.84)

SMART Domains

Protein: ENSMUSP00000003461
Gene: ENSMUSG00000020456
AA Change: Y354C

Domain	Start	End	E-Value	Type
Blast:Transket_pyr	131	199	8e-13	BLAST
Pfam:E1_dh	256	582	1.4e-95	PFAM
Transket_pyr	651	865	3.44e-50	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000081894
AA Change: Y350C

PolyPhen 2 Score 0.014 (Sensitivity: 0.96; Specificity: 0.79)

SMART Domains

Protein: ENSMUSP00000080569
Gene: ENSMUSG00000020456
AA Change: Y350C

Domain	Start	End	E-Value	Type
Pfam:E1_dh	252	578	1e-96	PFAM
Transket_pyr	647	861	3.44e-50	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000093350
AA Change: Y365C

PolyPhen 2 Score 0.122 (Sensitivity: 0.93; Specificity: 0.86)

SMART Domains

Protein: ENSMUSP00000091041
Gene: ENSMUSG00000020456
AA Change: Y365C

Domain	Start	End	E-Value	Type
Pfam:2-oxogl_dehyd_N	47	87	6.6e-21	PFAM
Pfam:E1_dh	267	593	1.1e-101	PFAM
Transket_pyr	662	876	3.44e-50	SMART
Pfam:OxoGdeHyase_C	880	1025	8.7e-58	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000101554
AA Change: Y354C

PolyPhen 2 Score 0.072 (Sensitivity: 0.94; Specificity: 0.84)

SMART Domains

Protein: ENSMUSP00000099090
Gene: ENSMUSG00000020456
AA Change: Y354C

Domain	Start	End	E-Value	Type
Blast:Transket_pyr	131	199	8e-13	BLAST
Pfam:E1_dh	256	582	1.4e-95	PFAM
Transket_pyr	651	865	3.44e-50	SMART

Meta Mutation Damage Score

0.3674

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.5%
20x: 98.2%

Validation Efficiency

98% (58/59)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes one subunit of the 2-oxoglutarate dehydrogenase complex. This complex catalyzes the overall conversion of 2-oxoglutarate (alpha-ketoglutarate) to succinyl-CoA and CO(2) during the Krebs cycle. The protein is located in the mitochondrial matrix and uses thiamine pyrophosphate as a cofactor. A congenital deficiency in 2-oxoglutarate dehydrogenase activity is believed to lead to hypotonia, metabolic acidosis, and hyperlactatemia. Alternative splicing results in multiple transcript variants encoding distinct isoforms.[provided by RefSeq, Sep 2009]

Allele List at MGI

All alleles(34) : Gene trapped(34)

Other mutations in this stock

Total: 59 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
6030458C11Rik	T	C	15: 12,812,068	H270R	probably damaging	Het
Abcb1a	T	C	5: 8,701,628	I336T	probably benign	Het
Adam19	T	A	11: 46,112,875	F177I	probably benign	Het
Ankrd53	T	C	6: 83,768,173	V455A	probably damaging	Het
Arrdc1	A	G	2: 24,925,665	S415P	probably benign	Het
Atp10a	T	C	7: 58,797,352	L614P	probably benign	Het
C130060K24Rik	A	T	6: 65,456,336	N380I	probably benign	Het
Catsper1	G	T	19: 5,343,963	V668F	probably damaging	Het
Cluh	T	A	11: 74,661,918	D596E	probably damaging	Het
Cnot10	A	G	9: 114,615,107	S407P	probably benign	Het
Commd6	T	C	14: 101,634,350	T86A	probably damaging	Het
D5Ertd579e	A	T	5: 36,604,657		probably null	Het
Eif3l	A	G	15: 79,085,560	D252G	probably damaging	Het
Epha2	A	T	4: 141,328,468	S962C	probably damaging	Het
Fcho1	C	A	8: 71,714,425		probably null	Het
Fgf23	G	T	6: 127,073,216	G63C	probably damaging	Het
Flnc	A	T	6: 29,445,749	Y834F	probably damaging	Het
Gcn1l1	T	C	5: 115,588,110	L608P	probably damaging	Het
Hdac5	T	A	11: 102,202,276	E545V	probably damaging	Het
Hecw2	A	T	1: 53,937,132	M166K	probably benign	Het
Ikbkb	T	C	8: 22,665,893	D586G	probably damaging	Het
Il1f9	G	C	2: 24,188,621		probably null	Het
Ipo13	A	T	4: 117,904,911	I422N	possibly damaging	Het
Iqgap3	GGAGAG	GGAG	3: 88,112,771		probably null	Het
Kat6a	G	A	8: 22,932,361	A896T	probably benign	Het
Kif28	A	G	1: 179,735,994	I139T	probably damaging	Het
Klhl25	A	G	7: 75,866,342	E332G	probably damaging	Het
Krt8	C	T	15: 101,997,908	A389T	probably benign	Het
Msrb3	T	C	10: 120,784,106	S175G	probably benign	Het
Muc5ac	C	T	7: 141,809,744		probably benign	Het
Myo10	T	C	15: 25,805,659	Y1709H	probably benign	Het
Nckap5	A	G	1: 126,023,194	S1519P	probably benign	Het
Npnt	T	A	3: 132,909,910	D124V	probably damaging	Het
Nr1d1	A	T	11: 98,770,836		probably null	Het
Olfr1305	A	T	2: 111,872,961	I298N	possibly damaging	Het
Phf21b	A	T	15: 84,787,446	C416S	probably damaging	Het
Prpsap1	A	G	11: 116,471,438	S373P	probably damaging	Het
Rab28	T	C	5: 41,703,534	T26A	probably damaging	Het
Rbbp8nl	A	G	2: 180,279,226	I455T	probably benign	Het
Rnft2	G	A	5: 118,228,818	A285V	possibly damaging	Het
Rrp36	G	T	17: 46,672,371	Q106K	probably benign	Het
Rsf1	CG	CGACGGCGGAG	7: 97,579,908		probably benign	Het
Runx2	G	A	17: 44,814,192	P80L	probably damaging	Het
Scn5a	A	G	9: 119,486,644	L1666P	probably damaging	Het
Siglecf	A	C	7: 43,355,200	T318P	probably benign	Het
Slc22a1	C	T	17: 12,667,305	W147*	probably null	Het
Smchd1	T	C	17: 71,353,506	I1868V	probably damaging	Het
Snx21	A	G	2: 164,791,902	S203G	probably damaging	Het
Srl	T	C	16: 4,482,831	K792R	probably benign	Het
Srrt	A	G	5: 137,298,673	F100S	probably benign	Het
Stard9	G	T	2: 120,697,436	M1391I	probably benign	Het
Syne2	A	G	12: 76,035,630	E119G	probably damaging	Het
Syt11	G	T	3: 88,762,155	S143R	possibly damaging	Het
Tiparp	T	A	3: 65,531,642	H126Q	probably benign	Het
Tulp2	C	A	7: 45,518,614	T150K	probably benign	Het
Ugt2b37	T	A	5: 87,242,429	Y386F	probably benign	Het
Usp31	C	T	7: 121,649,640	W860*	probably null	Het
Zfp317	A	G	9: 19,643,665	R30G	probably damaging	Het
Zfp709	C	A	8: 71,889,007	N93K	possibly damaging	Het

Other mutations in Ogdh

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01109:Ogdh	APN	11	6348790	missense	probably damaging	1.00
IGL01503:Ogdh	APN	11	6355069	missense	probably damaging	1.00
IGL01684:Ogdh	APN	11	6342546	missense	probably damaging	1.00
IGL02141:Ogdh	APN	11	6355015	missense	probably damaging	1.00
IGL02313:Ogdh	APN	11	6355400	missense	probably damaging	0.98
IGL02818:Ogdh	APN	11	6348270	missense	probably benign
N/A - 535:Ogdh	UTSW	11	6324911	missense	possibly damaging	0.60
PIT4498001:Ogdh	UTSW	11	6340504	missense	probably benign	0.09
R0328:Ogdh	UTSW	11	6347216	missense	probably benign	0.01
R0505:Ogdh	UTSW	11	6339936	splice site	probably benign
R0627:Ogdh	UTSW	11	6347216	missense	possibly damaging	0.78
R1119:Ogdh	UTSW	11	6340544	missense	probably damaging	1.00
R1480:Ogdh	UTSW	11	6347827	critical splice acceptor site	probably null
R1591:Ogdh	UTSW	11	6349384	missense	probably damaging	1.00
R1804:Ogdh	UTSW	11	6338565	missense	probably damaging	1.00
R1873:Ogdh	UTSW	11	6340438	splice site	probably benign
R1959:Ogdh	UTSW	11	6346638	missense	possibly damaging	0.49
R2004:Ogdh	UTSW	11	6334626	missense	possibly damaging	0.90
R2080:Ogdh	UTSW	11	6349393	missense	probably benign	0.00
R2384:Ogdh	UTSW	11	6342526	missense	probably damaging	1.00
R2656:Ogdh	UTSW	11	6348678	missense	probably benign
R2883:Ogdh	UTSW	11	6334545	missense	probably damaging	1.00
R3405:Ogdh	UTSW	11	6349462	missense	probably damaging	1.00
R3838:Ogdh	UTSW	11	6338627	nonsense	probably null
R3933:Ogdh	UTSW	11	6342601	missense	possibly damaging	0.72
R3939:Ogdh	UTSW	11	6350655	nonsense	probably null
R4296:Ogdh	UTSW	11	6349374	missense	probably damaging	0.97
R4393:Ogdh	UTSW	11	6316772	missense	probably damaging	1.00
R4427:Ogdh	UTSW	11	6355421	missense	probably benign	0.01
R4667:Ogdh	UTSW	11	6340600	missense	probably benign	0.20
R4669:Ogdh	UTSW	11	6340600	missense	probably benign	0.20
R4728:Ogdh	UTSW	11	6342549	missense	probably damaging	1.00
R4737:Ogdh	UTSW	11	6297044	missense	probably benign
R4785:Ogdh	UTSW	11	6349875	missense	probably damaging	1.00
R4796:Ogdh	UTSW	11	6340570	missense	probably benign	0.01
R5333:Ogdh	UTSW	11	6352126	missense	probably damaging	1.00
R5592:Ogdh	UTSW	11	6316763	splice site	probably null
R6318:Ogdh	UTSW	11	6349390	missense	probably damaging	0.99
R6988:Ogdh	UTSW	11	6313806	nonsense	probably null
R7406:Ogdh	UTSW	11	6348351	missense	probably benign	0.00
R7724:Ogdh	UTSW	11	6324887	missense	probably benign
R7763:Ogdh	UTSW	11	6338558	missense	probably benign
R7909:Ogdh	UTSW	11	6313965	missense	possibly damaging	0.55
R8207:Ogdh	UTSW	11	6349329	missense	probably benign	0.38
R8348:Ogdh	UTSW	11	6342619	missense	probably damaging	0.98
R8401:Ogdh	UTSW	11	6297174	nonsense	probably null
R8448:Ogdh	UTSW	11	6342619	missense	probably damaging	0.98
R8770:Ogdh	UTSW	11	6355336	missense	probably damaging	1.00
R8796:Ogdh	UTSW	11	6347129	missense	possibly damaging	0.75
R9132:Ogdh	UTSW	11	6340488	missense	probably benign	0.01
R9328:Ogdh	UTSW	11	6347838	missense	probably benign	0.30
R9479:Ogdh	UTSW	11	6347854	missense	possibly damaging	0.89
Z1088:Ogdh	UTSW	11	6355427	missense	probably benign
Z1177:Ogdh	UTSW	11	6297051	missense	probably benign
Z1177:Ogdh	UTSW	11	6316982	missense	probably benign	0.07

Predicted Primers

PCR Primer
(F):5'- TTGCCATTGAGAGTGAACCTC -3'
(R):5'- TACTCACAGACCTCTTAGGGG -3'

Sequencing Primer
(F):5'- GAGTGAACCTCTCCAACCAAC -3'
(R):5'- AGACCTCTTAGGGGCCTCAC -3'

Posted On

2018-10-18