Mutagenetix > Incidental Mutation

Incidental Mutation 'R4077:Lias'

316615

Institutional Source

Beutler Lab

Gene Symbol

Lias

Ensembl Gene

ENSMUSG00000029199

Gene Name

lipoic acid synthetase

Synonyms

7a5ex, 2900022L22Rik, 4933425M12Rik, mLip1, MGC7254

MMRRC Submission

041622-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R4077 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

65548840-65567766 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to T at 65552768 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Threonine to Serine at position 124 (T124S)

Ref Sequence

ENSEMBL: ENSMUSP00000113228 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000031101] [ENSMUST00000057885] [ENSMUST00000118543] [ENSMUST00000120094] [ENSMUST00000122026] [ENSMUST00000200374] [ENSMUST00000127874]

AlphaFold

Q99M04

Predicted Effect

probably benign
Transcript: ENSMUST00000031101
AA Change: T40S

PolyPhen 2 Score 0.124 (Sensitivity: 0.93; Specificity: 0.86)

SMART Domains

Protein: ENSMUSP00000031101
Gene: ENSMUSG00000029199
AA Change: T40S

Domain	Start	End	E-Value	Type
Pfam:LIAS_N	4	110	5.8e-49	PFAM
Elp3	126	332	1.42e-17	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000057885

SMART Domains

Protein: ENSMUSP00000109399
Gene: ENSMUSG00000047215

Domain	Start	End	E-Value	Type
Pfam:Ribosomal_L6	12	87	8.1e-18	PFAM
Pfam:Ribosomal_L6	99	178	7.4e-17	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000118543

SMART Domains

Protein: ENSMUSP00000113391
Gene: ENSMUSG00000047215

Domain	Start	End	E-Value	Type
Pfam:Ribosomal_L6	12	87	1.1e-19	PFAM
Pfam:Ribosomal_L6	99	165	1.5e-11	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000120094

SMART Domains

Protein: ENSMUSP00000113704
Gene: ENSMUSG00000047215

Domain	Start	End	E-Value	Type
Pfam:Ribosomal_L6	12	87	3e-17	PFAM
Pfam:Ribosomal_L6	99	178	2.9e-16	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000122026
AA Change: T124S

PolyPhen 2 Score 0.157 (Sensitivity: 0.92; Specificity: 0.87)

SMART Domains

Protein: ENSMUSP00000113228
Gene: ENSMUSG00000029199
AA Change: T124S

Domain	Start	End	E-Value	Type
Elp3	42	248	1.42e-17	SMART

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000126036

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000127519

Predicted Effect

probably benign
Transcript: ENSMUST00000200374
AA Change: T40S

PolyPhen 2 Score 0.012 (Sensitivity: 0.96; Specificity: 0.78)

SMART Domains

Protein: ENSMUSP00000143152
Gene: ENSMUSG00000029199
AA Change: T40S

Domain	Start	End	E-Value	Type
Blast:Elp3	2	54	5e-18	BLAST

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000139847

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000140879

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000128074

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000147660

Predicted Effect

probably benign
Transcript: ENSMUST00000196667

Predicted Effect

probably benign
Transcript: ENSMUST00000150815

Predicted Effect

probably benign
Transcript: ENSMUST00000127874

SMART Domains

Protein: ENSMUSP00000115577
Gene: ENSMUSG00000047215

Domain	Start	End	E-Value	Type
Pfam:Ribosomal_L6	12	80	3.2e-16	PFAM

Meta Mutation Damage Score

0.0760

Coding Region Coverage

1x: 99.2%
3x: 98.7%
10x: 97.5%
20x: 95.8%

Validation Efficiency

99% (81/82)

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 biotin and lipoic acid synthetases family. It localizes in mitochondrion and plays an important role in alpha-(+)-lipoic acid synthesis. It may also function in the sulfur insertion chemistry in lipoate biosynthesis. Alternative splicing occurs at this locus and two transcript variants encoding distinct isoforms have been identified. [provided by RefSeq, Jul 2008]
PHENOTYPE: Mice homozygous for a gene trap allele die before weaning. Embryos homozygous for a null allele become growth arrested and die at E7.5-E9.5. Embryos homozygous for an ENU allele survive to E12.5 showing a growth delay, an open neural tube, microcephaly, dilated hearts and lack of dorsal forebrain. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 71 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abhd12	T	A	2: 150,690,379 (GRCm39)		probably null	Het
Adam33	T	C	2: 130,905,444 (GRCm39)		probably benign	Het
Adrm1b	A	C	3: 92,336,195 (GRCm39)		probably benign	Het
Akap8	C	T	17: 32,531,272 (GRCm39)	R380Q	probably damaging	Het
Arhgef12	T	C	9: 42,886,588 (GRCm39)	M1131V	probably damaging	Het
Atrn	T	C	2: 130,806,850 (GRCm39)		probably null	Het
Btaf1	A	G	19: 36,963,879 (GRCm39)	T817A	probably benign	Het
C3	C	T	17: 57,512,303 (GRCm39)	D1542N	possibly damaging	Het
Cadm3	A	G	1: 173,169,236 (GRCm39)	V293A	probably benign	Het
Cdk11b	C	T	4: 155,724,204 (GRCm39)		probably benign	Het
Cdnf	A	G	2: 3,522,060 (GRCm39)	Y84C	probably damaging	Het
Chdh	T	C	14: 29,757,297 (GRCm39)	S407P	probably damaging	Het
Cmtr1	C	A	17: 29,904,949 (GRCm39)	T300K	probably damaging	Het
Dennd2d	A	T	3: 106,389,939 (GRCm39)		probably benign	Het
Diaph1	T	A	18: 37,986,636 (GRCm39)	E1116D	possibly damaging	Het
Eif1ad3	A	G	12: 87,843,401 (GRCm39)	K16R	unknown	Het
Eif1ad3	A	T	12: 87,843,710 (GRCm39)	D119V	possibly damaging	Het
Enpp1	A	G	10: 24,544,905 (GRCm39)		probably null	Het
Erbb4	T	C	1: 68,079,496 (GRCm39)	T1195A	probably benign	Het
Ermard	T	A	17: 15,273,638 (GRCm39)	S408T	probably benign	Het
Etl4	A	T	2: 20,812,772 (GRCm39)	R1442S	probably damaging	Het
F13b	T	A	1: 139,429,508 (GRCm39)	F9I	unknown	Het
Fnbp4	C	T	2: 90,588,821 (GRCm39)	R531*	probably null	Het
Gdf6	A	G	4: 9,844,776 (GRCm39)	Y100C	probably damaging	Het
Gpr3	T	C	4: 132,938,226 (GRCm39)	T149A	probably damaging	Het
Grm8	T	C	6: 27,760,208 (GRCm39)	H374R	probably benign	Het
Hbs1l	T	C	10: 21,228,501 (GRCm39)	V493A	probably damaging	Het
Hgs	A	G	11: 120,368,202 (GRCm39)	K277E	probably damaging	Het
Hnrnpul1	C	T	7: 25,426,300 (GRCm39)	R517Q	probably damaging	Het
Hoxa11	A	T	6: 52,222,504 (GRCm39)	Y66N	probably damaging	Het
Hsh2d	G	A	8: 72,954,304 (GRCm39)	D229N	probably benign	Het
Igdcc4	T	A	9: 65,039,047 (GRCm39)	L944Q	probably damaging	Het
Ighv3-1	C	A	12: 113,928,107 (GRCm39)	S84I	probably damaging	Het
Iqgap2	T	C	13: 95,794,375 (GRCm39)	D1199G	probably damaging	Het
Kcnk10	A	T	12: 98,401,205 (GRCm39)	M490K	probably benign	Het
Kirrel1	A	G	3: 86,992,387 (GRCm39)		probably null	Het
Lrig3	A	C	10: 125,845,656 (GRCm39)	E695A	probably damaging	Het
Lrpap1	A	G	5: 35,253,381 (GRCm39)	I261T	possibly damaging	Het
Lrrc37a	T	A	11: 103,388,808 (GRCm39)	T2206S	unknown	Het
Macf1	T	A	4: 123,365,884 (GRCm39)	Q2959L	probably benign	Het
Mis12	A	G	11: 70,916,134 (GRCm39)	T56A	probably benign	Het
Or10ag56	T	A	2: 87,139,208 (GRCm39)	M25K	probably null	Het
Or1l4	T	A	2: 37,092,024 (GRCm39)	I257N	possibly damaging	Het
Or4k41	A	G	2: 111,279,848 (GRCm39)	D121G	probably damaging	Het
Or5b99	T	C	19: 12,977,235 (GRCm39)	V295A	probably damaging	Het
Otof	A	T	5: 30,576,850 (GRCm39)	L134Q	possibly damaging	Het
Pds5b	T	A	5: 150,717,824 (GRCm39)	V1155E	possibly damaging	Het
Pdss2	A	T	10: 43,278,518 (GRCm39)	M342L	probably benign	Het
Phyhipl	C	T	10: 70,404,903 (GRCm39)	V57I	probably damaging	Het
Plekha5	T	A	6: 140,501,647 (GRCm39)		probably null	Het
Pnck	A	T	X: 72,701,761 (GRCm39)	V93E	probably damaging	Het
Proser1	A	G	3: 53,385,962 (GRCm39)	T615A	probably damaging	Het
Ptprk	G	A	10: 28,139,508 (GRCm39)	V78I	probably benign	Het
Ptprv	A	G	1: 135,038,168 (GRCm39)		noncoding transcript	Het
Ranbp3l	A	G	15: 9,060,838 (GRCm39)	N233S	probably damaging	Het
Rassf2	G	A	2: 131,854,522 (GRCm39)	P7S	probably benign	Het
Sart1	A	T	19: 5,432,771 (GRCm39)	L521Q	possibly damaging	Het
Scgb1b21	T	A	7: 33,227,118 (GRCm39)		noncoding transcript	Het
Scyl2	A	T	10: 89,476,458 (GRCm39)	M889K	probably benign	Het
Secisbp2l	A	G	2: 125,593,785 (GRCm39)		probably benign	Het
Svil	A	G	18: 5,063,522 (GRCm39)	E931G	probably benign	Het
Syce1	C	A	7: 140,359,809 (GRCm39)	L83F	probably damaging	Het
Tdrd1	A	G	19: 56,819,505 (GRCm39)	M2V	probably benign	Het
Tjp2	A	T	19: 24,086,182 (GRCm39)	V780E	possibly damaging	Het
Tram1	A	G	1: 13,636,599 (GRCm39)	V358A	probably benign	Het
Unc13c	C	T	9: 73,643,821 (GRCm39)	W1214*	probably null	Het
Vps13b	T	C	15: 35,455,274 (GRCm39)	C728R	probably damaging	Het
Wwox	A	G	8: 115,166,481 (GRCm39)		probably benign	Het
Zbtb41	G	A	1: 139,357,064 (GRCm39)	V440I	probably benign	Het
Zfp777	T	C	6: 48,002,456 (GRCm39)	S589G	probably benign	Het
Zfp955a	A	G	17: 33,460,675 (GRCm39)	Y486H	probably benign	Het

Other mutations in Lias

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01704:Lias	APN	5	65,562,673 (GRCm39)	missense	probably damaging	1.00
IGL02473:Lias	APN	5	65,562,745 (GRCm39)	missense	possibly damaging	0.95
R6812_Lias_838	UTSW	5	65,566,132 (GRCm39)	missense	possibly damaging	0.76
R1480:Lias	UTSW	5	65,549,634 (GRCm39)	missense	probably benign
R1677:Lias	UTSW	5	65,548,981 (GRCm39)	missense	probably damaging	1.00
R1836:Lias	UTSW	5	65,549,686 (GRCm39)	missense	probably benign
R4438:Lias	UTSW	5	65,552,787 (GRCm39)	missense	probably damaging	1.00
R4458:Lias	UTSW	5	65,551,383 (GRCm39)	splice site	probably null
R4710:Lias	UTSW	5	65,555,070 (GRCm39)	missense	probably benign	0.09
R6050:Lias	UTSW	5	65,551,315 (GRCm39)	missense	possibly damaging	0.47
R6812:Lias	UTSW	5	65,566,132 (GRCm39)	missense	possibly damaging	0.76
R8734:Lias	UTSW	5	65,561,552 (GRCm39)	missense	probably damaging	1.00
R8751:Lias	UTSW	5	65,557,193 (GRCm39)	missense	probably benign	0.05
R9233:Lias	UTSW	5	65,551,331 (GRCm39)	missense	probably benign	0.02
X0061:Lias	UTSW	5	65,549,703 (GRCm39)	missense	probably benign	0.00

Predicted Primers

PCR Primer
(F):5'- AGGACCTTCAGAAGAGCAGTCG -3'
(R):5'- ACAACGAGTGTCAAGACGGC -3'

Sequencing Primer
(F):5'- AGTCGGTGCTCTTAACCACTGAG -3'
(R):5'- AAGACGGCCAGGTTCTCTCTTTG -3'

Posted On

2015-05-15