Mutagenetix > Incidental Mutation

Incidental Mutation 'R4788:Hmgcs2'

367228

Institutional Source

Beutler Lab

Gene Symbol

Hmgcs2

Ensembl Gene

ENSMUSG00000027875

Gene Name

3-hydroxy-3-methylglutaryl-Coenzyme A synthase 2

Synonyms

mHS

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.110) question?

Stock #

R4788 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

98187751-98218054 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 98198400 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Aspartic acid to Glycine at position 101 (D101G)

Ref Sequence

ENSEMBL: ENSMUSP00000113296 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000090746] [ENSMUST00000120541]

AlphaFold

P54869

Predicted Effect

probably damaging
Transcript: ENSMUST00000090746
AA Change: D101G

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000088249
Gene: ENSMUSG00000027875
AA Change: D101G

Domain	Start	End	E-Value	Type
Pfam:HMG_CoA_synt_N	50	223	2.9e-111	PFAM
Pfam:HMG_CoA_synt_C	224	506	6.6e-131	PFAM

Predicted Effect

probably damaging
Transcript: ENSMUST00000120541
AA Change: D101G

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000113296
Gene: ENSMUSG00000027875
AA Change: D101G

Domain	Start	End	E-Value	Type
Pfam:HMG_CoA_synt_N	50	223	7.2e-108	PFAM
Pfam:HMG_CoA_synt_C	224	506	1.8e-131	PFAM

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000196040

Coding Region Coverage

1x: 98.8%
3x: 98.4%
10x: 96.9%
20x: 94.4%

Validation Efficiency

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The protein encoded by this gene belongs to the HMG-CoA synthase family. It is a mitochondrial enzyme that catalyzes the first reaction of ketogenesis, a metabolic pathway that provides lipid-derived energy for various organs during times of carbohydrate deprivation, such as fasting. Mutations in this gene are associated with HMG-CoA synthase deficiency. Alternatively spliced transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Oct 2009]

Allele List at MGI

Other mutations in this stock

Total: 68 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abca4	G	A	3: 121,960,361 (GRCm39)	D815N	probably damaging	Het
Abcc9	A	T	6: 142,566,456 (GRCm39)	C1135*	probably null	Het
Ap3b1	G	A	13: 94,702,149 (GRCm39)	M1067I	unknown	Het
Arhgap15	T	C	2: 43,638,902 (GRCm39)	M1T	probably null	Het
Boc	T	C	16: 44,320,796 (GRCm39)	D288G	probably damaging	Het
Brsk1	G	T	7: 4,701,954 (GRCm39)		probably null	Het
Cabp1	T	C	5: 115,313,530 (GRCm39)	N226S	probably benign	Het
Capn13	A	T	17: 73,644,427 (GRCm39)	Y367*	probably null	Het
Ccdc191	A	G	16: 43,777,185 (GRCm39)	E632G	probably damaging	Het
Cit	T	C	5: 116,071,565 (GRCm39)	S591P	probably damaging	Het
Ckmt1	T	C	2: 121,190,427 (GRCm39)	V118A	possibly damaging	Het
Cndp2	T	C	18: 84,693,289 (GRCm39)	N157S	probably damaging	Het
Col6a3	A	G	1: 90,700,672 (GRCm39)		probably null	Het
Coq2	A	T	5: 100,805,775 (GRCm39)	V287E	probably damaging	Het
Cpa6	T	C	1: 10,478,502 (GRCm39)	K278R	possibly damaging	Het
Cracdl	A	T	1: 37,670,556 (GRCm39)	I128K	probably damaging	Het
Cybb	C	G	X: 9,316,989 (GRCm39)	D246H	probably benign	Het
Cyp3a25	A	T	5: 145,921,892 (GRCm39)	Y347*	probably null	Het
Dcun1d4	G	T	5: 73,691,971 (GRCm39)	W160L	probably damaging	Het
Dennd4c	A	G	4: 86,738,200 (GRCm39)	T994A	probably benign	Het
Dhx57	T	C	17: 80,582,760 (GRCm39)	T229A	probably benign	Het
Dnah6	T	A	6: 73,106,513 (GRCm39)	R1741S	probably damaging	Het
Dock1	T	A	7: 134,747,213 (GRCm39)	V1508D	probably damaging	Het
Donson	T	C	16: 91,484,721 (GRCm39)	T117A	possibly damaging	Het
Dtnb	A	G	12: 3,822,699 (GRCm39)	D533G	probably damaging	Het
Fcrl5	A	G	3: 87,364,495 (GRCm39)	N470S	probably damaging	Het
Focad	T	A	4: 88,275,706 (GRCm39)	V1105E	unknown	Het
Fry	T	C	5: 150,323,101 (GRCm39)	V1084A	probably benign	Het
Gabra1	G	T	11: 42,037,980 (GRCm39)	R213S	probably damaging	Het
Gbp2b	A	C	3: 142,317,171 (GRCm39)	K509T	probably benign	Het
Gprc6a	T	C	10: 51,491,104 (GRCm39)	T811A	probably benign	Het
Ifna11	G	A	4: 88,738,245 (GRCm39)	W17*	probably null	Het
Ighv1-62-3	T	A	12: 115,424,672 (GRCm39)	M100L	probably benign	Het
Lgmn	T	A	12: 102,368,936 (GRCm39)	Y181F	probably benign	Het
Map4k4	T	C	1: 40,043,076 (GRCm39)	S644P	probably benign	Het
Med9	T	A	11: 59,839,266 (GRCm39)	N58K	probably benign	Het
Nav1	C	T	1: 135,397,461 (GRCm39)	A903T	probably benign	Het
Nop53	T	C	7: 15,676,240 (GRCm39)	E153G	possibly damaging	Het
Nop56	G	T	2: 130,120,820 (GRCm39)	V190L	probably benign	Het
Nyap2	A	T	1: 81,247,112 (GRCm39)	M687L	probably benign	Het
Or4a81	G	A	2: 89,619,480 (GRCm39)	S72F	probably damaging	Het
Or8g17	T	C	9: 38,930,217 (GRCm39)	T207A	probably benign	Het
Or8g26	A	G	9: 39,095,908 (GRCm39)	T145A	probably benign	Het
Osbp2	T	C	11: 3,813,320 (GRCm39)	K183R	probably benign	Het
Pappa2	A	G	1: 158,611,487 (GRCm39)	V1492A	possibly damaging	Het
Pax1	A	G	2: 147,208,124 (GRCm39)	Q244R	possibly damaging	Het
Pcdh9	C	A	14: 94,124,851 (GRCm39)	V317F	probably damaging	Het
Pkhd1l1	A	T	15: 44,361,417 (GRCm39)	Q489L	probably damaging	Het
Poln	A	T	5: 34,286,675 (GRCm39)	S164R	probably benign	Het
Ptf1a	T	C	2: 19,450,762 (GRCm39)	S31P	probably benign	Het
Rasal3	A	T	17: 32,618,312 (GRCm39)	D164E	probably benign	Het
Rnf170	A	G	8: 26,630,891 (GRCm39)	E168G	probably damaging	Het
Rubcn	A	G	16: 32,656,778 (GRCm39)		probably null	Het
Sec16b	A	T	1: 157,389,094 (GRCm39)	T830S	possibly damaging	Het
Sel1l3	A	G	5: 53,289,175 (GRCm39)	V882A	probably benign	Het
Sfpq	A	G	4: 126,919,791 (GRCm39)	E512G	probably damaging	Het
Sh3pxd2a	A	G	19: 47,302,518 (GRCm39)	L187P	probably damaging	Het
Skint6	C	T	4: 113,095,533 (GRCm39)	G42D	possibly damaging	Het
Slc7a2	A	G	8: 41,367,023 (GRCm39)	I526V	probably benign	Het
Spmip7	T	C	11: 11,438,652 (GRCm39)		probably null	Het
Ssh2	A	T	11: 77,320,624 (GRCm39)	N328Y	probably damaging	Het
Taok2	G	A	7: 126,467,304 (GRCm39)	S167L	possibly damaging	Het
Tom1l2	A	G	11: 60,139,844 (GRCm39)	L275P	probably damaging	Het
Trgv5	A	G	13: 19,376,724 (GRCm39)	K57R	probably benign	Het
Tyrp1	C	T	4: 80,763,180 (GRCm39)	R356*	probably null	Het
Zan	A	G	5: 137,440,375 (GRCm39)	L1953P	unknown	Het
Zfhx3	T	C	8: 109,520,842 (GRCm39)	S655P	probably damaging	Het
Zmym1	T	C	4: 126,948,090 (GRCm39)	T94A	probably benign	Het

Other mutations in Hmgcs2

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
R0579:Hmgcs2	UTSW	3	98,198,264 (GRCm39)	missense	probably damaging	1.00
R0657:Hmgcs2	UTSW	3	98,198,369 (GRCm39)	missense	probably benign
R0724:Hmgcs2	UTSW	3	98,204,317 (GRCm39)	nonsense	probably null
R2024:Hmgcs2	UTSW	3	98,206,530 (GRCm39)	missense	probably damaging	1.00
R2109:Hmgcs2	UTSW	3	98,204,337 (GRCm39)	nonsense	probably null
R2202:Hmgcs2	UTSW	3	98,198,499 (GRCm39)	missense	probably damaging	1.00
R2203:Hmgcs2	UTSW	3	98,198,499 (GRCm39)	missense	probably damaging	1.00
R2204:Hmgcs2	UTSW	3	98,198,499 (GRCm39)	missense	probably damaging	1.00
R2205:Hmgcs2	UTSW	3	98,198,499 (GRCm39)	missense	probably damaging	1.00
R3758:Hmgcs2	UTSW	3	98,198,406 (GRCm39)	missense	probably damaging	1.00
R3779:Hmgcs2	UTSW	3	98,206,428 (GRCm39)	splice site	probably benign
R3958:Hmgcs2	UTSW	3	98,204,793 (GRCm39)	missense	possibly damaging	0.48
R3959:Hmgcs2	UTSW	3	98,204,793 (GRCm39)	missense	possibly damaging	0.48
R3960:Hmgcs2	UTSW	3	98,204,793 (GRCm39)	missense	possibly damaging	0.48
R3962:Hmgcs2	UTSW	3	98,198,354 (GRCm39)	missense	possibly damaging	0.91
R5102:Hmgcs2	UTSW	3	98,187,786 (GRCm39)	start gained	probably benign
R5708:Hmgcs2	UTSW	3	98,198,478 (GRCm39)	missense	probably damaging	1.00
R5742:Hmgcs2	UTSW	3	98,204,832 (GRCm39)	missense	probably benign
R7268:Hmgcs2	UTSW	3	98,204,796 (GRCm39)	missense	probably benign	0.02
R7294:Hmgcs2	UTSW	3	98,198,211 (GRCm39)	missense	probably benign	0.09
R7503:Hmgcs2	UTSW	3	98,209,940 (GRCm39)	missense	probably damaging	1.00
R7767:Hmgcs2	UTSW	3	98,198,582 (GRCm39)	missense	probably damaging	1.00
R8043:Hmgcs2	UTSW	3	98,198,444 (GRCm39)	missense	probably damaging	1.00
R8360:Hmgcs2	UTSW	3	98,204,724 (GRCm39)	missense	possibly damaging	0.68
R8931:Hmgcs2	UTSW	3	98,203,557 (GRCm39)	missense	probably damaging	1.00
R9167:Hmgcs2	UTSW	3	98,204,430 (GRCm39)	missense	possibly damaging	0.46
R9183:Hmgcs2	UTSW	3	98,198,232 (GRCm39)	missense	possibly damaging	0.67
R9211:Hmgcs2	UTSW	3	98,204,748 (GRCm39)	missense	possibly damaging	0.95
Z1176:Hmgcs2	UTSW	3	98,198,261 (GRCm39)	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- GGCCAAAACAGATACATGGC -3'
(R):5'- CCAGTTGGCAGCATTGAAGAG -3'

Sequencing Primer
(F):5'- TACATGGCCAAAAGATGTGGGC -3'
(R):5'- GGTATCTATGCCCTCGATGTCAG -3'

Posted On

2015-12-29