Mutagenetix > Incidental Mutation

Incidental Mutation 'R7294:Hmgcs2'

566606

Institutional Source

Beutler Lab

Gene Symbol

Hmgcs2

Ensembl Gene

ENSMUSG00000027875

Gene Name

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

Synonyms

mHS

MMRRC Submission

045399-MU

Accession Numbers

Essential gene?

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

Stock #

R7294 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

98187751-98218054 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

C to T at 98198211 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Threonine to Isoleucine at position 38 (T38I)

Ref Sequence

ENSEMBL: ENSMUSP00000088249 (fasta)

Gene Model

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

AlphaFold

P54869

Predicted Effect

probably benign
Transcript: ENSMUST00000090746
AA Change: T38I

PolyPhen 2 Score 0.093 (Sensitivity: 0.93; Specificity: 0.85)

SMART Domains

Protein: ENSMUSP00000088249
Gene: ENSMUSG00000027875
AA Change: T38I

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 benign
Transcript: ENSMUST00000120541
AA Change: T38I

PolyPhen 2 Score 0.093 (Sensitivity: 0.93; Specificity: 0.85)

SMART Domains

Protein: ENSMUSP00000113296
Gene: ENSMUSG00000027875
AA Change: T38I

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

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.7%
20x: 99.0%

Validation Efficiency

94% (49/52)

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: 52 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
A2m	T	A	6: 121,650,541 (GRCm39)	Y1216*	probably null	Het
Abca17	G	A	17: 24,539,983 (GRCm39)	T415M	not run	Het
Adam1a	G	T	5: 121,658,068 (GRCm39)	C408*	probably null	Het
Adamts9	G	A	6: 92,871,270 (GRCm39)	T603M	probably damaging	Het
Amdhd1	T	C	10: 93,370,301 (GRCm39)	E179G	probably benign	Het
Bcan	T	C	3: 87,902,831 (GRCm39)	T316A	possibly damaging	Het
Bpifb9a	C	T	2: 154,109,616 (GRCm39)	T504M	probably damaging	Het
C5ar1	T	C	7: 15,982,950 (GRCm39)	I23M	probably benign	Het
Cd109	A	T	9: 78,619,917 (GRCm39)	E1386D	probably damaging	Het
Cdcp1	C	T	9: 123,006,986 (GRCm39)	C587Y	probably benign	Het
Cdh22	A	C	2: 164,984,013 (GRCm39)	V413G	possibly damaging	Het
Cfap44	A	G	16: 44,225,256 (GRCm39)		probably benign	Het
Col2a1	A	G	15: 97,885,168 (GRCm39)		probably null	Het
Col6a3	A	T	1: 90,756,005 (GRCm39)	Y95N	probably damaging	Het
Dusp13b	A	G	14: 21,783,782 (GRCm39)	S178P	possibly damaging	Het
Fhod3	A	G	18: 25,266,037 (GRCm39)	E1575G	probably damaging	Het
Gfpt2	C	T	11: 49,709,435 (GRCm39)	R209*	probably null	Het
Heg1	T	C	16: 33,546,859 (GRCm39)	S573P	probably damaging	Het
Hinfp	A	G	9: 44,210,567 (GRCm39)	C152R	probably damaging	Het
Jakmip1	T	C	5: 37,274,804 (GRCm39)	F441L	possibly damaging	Het
Kcnj5	A	C	9: 32,234,045 (GRCm39)	L90R	probably damaging	Het
Kpna4	A	C	3: 68,999,956 (GRCm39)		probably null	Het
Krt15	T	A	11: 100,022,848 (GRCm39)	I456F	possibly damaging	Het
Leprotl1	A	T	8: 34,606,006 (GRCm39)		probably null	Het
Muc4	A	T	16: 32,576,835 (GRCm39)	T42S	possibly damaging	Het
Naa80	T	G	9: 107,460,182 (GRCm39)	F26V	possibly damaging	Het
Nr1h5	T	C	3: 102,852,578 (GRCm39)	T419A	probably benign	Het
Nutm1	G	A	2: 112,080,401 (GRCm39)	R505C	probably damaging	Het
Or4c12	A	C	2: 89,774,068 (GRCm39)	Y130*	probably null	Het
Or52b3	T	A	7: 102,204,160 (GRCm39)	I223N	probably damaging	Het
Pax6	T	A	2: 105,515,246 (GRCm39)	C66*	probably null	Het
Pde10a	A	T	17: 8,975,853 (GRCm39)	N53Y	probably benign	Het
Pdgfra	A	G	5: 75,342,312 (GRCm39)	N711S	probably benign	Het
Rimkla	A	T	4: 119,325,663 (GRCm39)	S249T	probably damaging	Het
Rsf1	CGGCGGCGG	CGGCGGCGGGGGCGGCGG	7: 97,229,127 (GRCm39)		probably benign	Het
Scn3a	A	G	2: 65,302,685 (GRCm39)	S1254P	probably damaging	Het
Slc26a1	G	T	5: 108,821,698 (GRCm39)	R80S	possibly damaging	Het
Slc2a4	T	C	11: 69,836,225 (GRCm39)	D262G	probably benign	Het
Specc1	T	A	11: 62,009,163 (GRCm39)	S226R	probably benign	Het
Srsf4	A	G	4: 131,627,772 (GRCm39)	S289G	unknown	Het
Stil	T	C	4: 114,864,480 (GRCm39)	V127A	probably benign	Het
Syne1	A	T	10: 5,047,483 (GRCm39)		probably null	Het
Tbc1d22a	T	A	15: 86,196,036 (GRCm39)	Y336N	possibly damaging	Het
Tbc1d8	C	T	1: 39,445,843 (GRCm39)	G116E	probably damaging	Het
Thrb	A	G	14: 17,826,963 (GRCm38)		probably benign	Het
Timd5	T	A	11: 46,426,439 (GRCm39)	I182K	probably benign	Het
Tln1	G	T	4: 43,534,399 (GRCm39)	H2253Q	probably benign	Het
Tmem131	A	C	1: 36,893,928 (GRCm39)	N158K	possibly damaging	Het
Toporsl	A	C	4: 52,611,903 (GRCm39)	T599P	probably benign	Het
Tpr	C	T	1: 150,279,638 (GRCm39)	R256C	probably damaging	Het
Triobp	C	T	15: 78,858,176 (GRCm39)	A1259V	probably damaging	Het
Zfp40	A	G	17: 23,395,411 (GRCm39)	I392T	possibly damaging	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
R4788:Hmgcs2	UTSW	3	98,198,400 (GRCm39)	missense	probably damaging	1.00
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
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'- GTCGGACAGACTACCATACAAAGAATG -3'
(R):5'- TGAACAGAAGCCCATACGG -3'

Sequencing Primer
(F):5'- CAAAGAATGAACCATACAATGTGTG -3'
(R):5'- GGGCTGGAAAATAGACCT -3'

Posted On

2019-06-26