Mutagenetix > Incidental Mutation

Incidental Mutation 'R9276:Amt'

703314

Institutional Source

Beutler Lab

Gene Symbol

Amt

Ensembl Gene

ENSMUSG00000032607

Gene Name

aminomethyltransferase

Synonyms

EG434437

MMRRC Submission

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R9276 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

108174104-108179501 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

C to A at 108178410 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Threonine to Lysine at position 339 (T339K)

Ref Sequence

ENSEMBL: ENSMUSP00000035230 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000007959] [ENSMUST00000035227] [ENSMUST00000035230] [ENSMUST00000044725] [ENSMUST00000192886] [ENSMUST00000195615]

AlphaFold

Q8CFA2

Predicted Effect

probably benign
Transcript: ENSMUST00000007959

SMART Domains

Protein: ENSMUSP00000007959
Gene: ENSMUSG00000007815

Domain	Start	End	E-Value	Type
RHO	8	181	1.09e-134	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000035227

Predicted Effect

probably benign
Transcript: ENSMUST00000035230
AA Change: T339K

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)

SMART Domains

Protein: ENSMUSP00000035230
Gene: ENSMUSG00000032607
AA Change: T339K

Domain	Start	End	E-Value	Type
Pfam:GCV_T	38	291	7.8e-86	PFAM
Pfam:GCV_T_C	300	392	1.6e-23	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000044725

SMART Domains

Protein: ENSMUSP00000045063
Gene: ENSMUSG00000039461

Domain	Start	End	E-Value	Type
Pfam:T_cell_tran_alt	15	122	1.3e-39	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000192886

SMART Domains

Protein: ENSMUSP00000142002
Gene: ENSMUSG00000039461

Domain	Start	End	E-Value	Type
Pfam:T_cell_tran_alt	15	106	1.5e-45	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000195615

SMART Domains

Protein: ENSMUSP00000141592
Gene: ENSMUSG00000039461

Domain	Start	End	E-Value	Type
Pfam:T_cell_tran_alt	15	103	2.9e-39	PFAM

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.6%
20x: 98.7%

Validation Efficiency

99% (83/84)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes one of four critical components of the glycine cleavage system. Mutations in this gene have been associated with glycine encephalopathy. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2011]
PHENOTYPE: Mice homozygous for a gene trapped allele develop neural tubes defects at high frequency and exhibit prenatal lethality. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 84 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
9630041A04Rik	A	T	9: 101,819,887 (GRCm39)	R102S	probably benign	Het
Abitram	A	T	4: 56,806,141 (GRCm39)	K184N	probably benign	Het
Acvr2b	C	T	9: 119,231,616 (GRCm39)	T2M	probably benign	Het
Adamtsl3	A	G	7: 82,206,710 (GRCm39)		probably benign	Het
Adcy7	A	G	8: 89,052,014 (GRCm39)	Y894C	probably damaging	Het
Afdn	T	A	17: 14,024,270 (GRCm39)	C59S	probably damaging	Het
Ankrd27	G	T	7: 35,319,995 (GRCm39)	V639L	probably benign	Het
Anxa10	G	T	8: 62,549,753 (GRCm39)	Q31K	probably damaging	Het
Ap1g2	T	C	14: 55,339,818 (GRCm39)	T454A	probably benign	Het
Boll	A	T	1: 55,399,812 (GRCm39)	I43N	possibly damaging	Het
Cacna1c	T	C	6: 118,601,394 (GRCm39)	D1472G		Het
Calcrl	T	C	2: 84,205,643 (GRCm39)	N16S	probably benign	Het
Ccdc191	C	T	16: 43,764,041 (GRCm39)	Q501*	probably null	Het
Cchcr1	T	C	17: 35,841,105 (GRCm39)	L658P	probably damaging	Het
Cfap46	A	T	7: 139,201,207 (GRCm39)	C1919S	unknown	Het
Col6a3	G	A	1: 90,735,403 (GRCm39)	L1356F	possibly damaging	Het
Dlc1	A	G	8: 37,046,558 (GRCm39)	S680P	possibly damaging	Het
Dock4	T	G	12: 40,699,404 (GRCm39)	M206R	possibly damaging	Het
Eml5	T	C	12: 98,765,060 (GRCm39)	K1630E	probably damaging	Het
Fat1	A	G	8: 45,488,514 (GRCm39)	T3432A	probably damaging	Het
Fcrl5	G	T	3: 87,343,138 (GRCm39)		probably benign	Het
Fcrla	A	G	1: 170,755,135 (GRCm39)		probably benign	Het
Fut4	C	A	9: 14,662,572 (GRCm39)	D241Y	probably benign	Het
Fzd6	A	G	15: 38,870,962 (GRCm39)		probably benign	Het
Gjc2	T	C	11: 59,068,453 (GRCm39)	T10A	probably damaging	Het
Gle1	C	T	2: 29,829,514 (GRCm39)	H203Y	possibly damaging	Het
Gm5565	A	T	5: 146,096,917 (GRCm39)	I74N	probably damaging	Het
Gnl2	T	A	4: 124,947,250 (GRCm39)	I624K	possibly damaging	Het
Gnpat	C	A	8: 125,614,524 (GRCm39)	N653K	probably benign	Het
Gstcd	A	G	3: 132,777,665 (GRCm39)	L382S	probably damaging	Het
Ipcef1	A	G	10: 6,857,936 (GRCm39)		probably benign	Het
Jmjd7	T	C	2: 119,860,895 (GRCm39)	V115A	possibly damaging	Het
Ltbp2	G	A	12: 84,837,864 (GRCm39)	P1192L	probably benign	Het
Ltbp2	T	G	12: 84,876,885 (GRCm39)	D440A	possibly damaging	Het
Macf1	T	G	4: 123,328,501 (GRCm39)	D4744A	probably damaging	Het
Mapk11	T	C	15: 89,029,372 (GRCm39)	D230G	probably damaging	Het
Mfsd6	A	C	1: 52,747,514 (GRCm39)	Y450*	probably null	Het
Mtmr9	A	G	14: 63,781,001 (GRCm39)	C30R	probably damaging	Het
Ncf1	G	A	5: 134,250,693 (GRCm39)	Q376*	probably null	Het
Ncor2	C	A	5: 125,113,150 (GRCm39)	R296M		Het
Or51ah3	A	T	7: 103,210,004 (GRCm39)	T107S	probably damaging	Het
Or5d37	A	G	2: 87,923,806 (GRCm39)	V158A	probably benign	Het
Or5k8	A	G	16: 58,644,734 (GRCm39)	F113L	probably benign	Het
Or8b57	A	T	9: 40,003,632 (GRCm39)	I210K	possibly damaging	Het
Or8b8	C	A	9: 37,809,415 (GRCm39)	S238R	probably benign	Het
Or8k31-ps1	A	T	2: 86,356,392 (GRCm39)	L43*	probably null	Het
Pate9	A	T	9: 36,445,727 (GRCm39)	C75S	probably damaging	Het
Pcsk6	A	T	7: 65,559,950 (GRCm39)	I92F	probably damaging	Het
Plec	A	G	15: 76,060,445 (GRCm39)	V3164A	probably benign	Het
Prss16	A	G	13: 22,190,175 (GRCm39)		probably benign	Het
Ptch2	T	A	4: 116,967,505 (GRCm39)	H724Q	probably damaging	Het
Pzp	A	T	6: 128,499,077 (GRCm39)	F190Y	probably damaging	Het
Rab6a	A	G	7: 100,275,809 (GRCm39)	T41A	probably benign	Het
Rbm6	A	G	9: 107,660,926 (GRCm39)	L879P	probably damaging	Het
Rem1	T	A	2: 152,469,969 (GRCm39)		probably benign	Het
Rnf17	T	C	14: 56,719,554 (GRCm39)	S935P	probably damaging	Het
Ryr1	C	A	7: 28,802,254 (GRCm39)	V789L	probably damaging	Het
Scgb2b3	A	T	7: 31,059,528 (GRCm39)	M82K	possibly damaging	Het
Sgce	T	A	6: 4,674,585 (GRCm39)	L451F	probably damaging	Het
Slc25a17	A	C	15: 81,207,814 (GRCm39)	V258G	probably benign	Het
Spidr	G	A	16: 15,784,712 (GRCm39)	T452I	probably benign	Het
Tas2r129	A	G	6: 132,928,576 (GRCm39)	N171S	probably benign	Het
Tbc1d24	A	T	17: 24,405,114 (GRCm39)	V10E	probably damaging	Het
Tdo2	T	G	3: 81,876,885 (GRCm39)	M115L	probably benign	Het
Tdrd9	T	C	12: 111,980,935 (GRCm39)		probably null	Het
Tead1	T	A	7: 112,493,601 (GRCm39)	I376N	probably damaging	Het
Tmem26	A	G	10: 68,614,488 (GRCm39)	H301R	possibly damaging	Het
Tnxb	A	G	17: 34,929,134 (GRCm39)	T2726A	possibly damaging	Het
Trim43c	T	C	9: 88,723,966 (GRCm39)	M164T	probably benign	Het
Trpc1	G	A	9: 95,590,288 (GRCm39)	S723L	probably benign	Het
Txndc15	A	G	13: 55,865,914 (GRCm39)	D126G	probably benign	Het
Urb1	C	T	16: 90,569,463 (GRCm39)		probably benign	Het
Usp25	C	T	16: 76,910,721 (GRCm39)	H926Y	probably benign	Het
Uvssa	T	A	5: 33,572,180 (GRCm39)	M700K	possibly damaging	Het
Vdac1	T	A	11: 52,274,789 (GRCm39)	Y146N	probably damaging	Het
Vmn1r231	A	T	17: 21,110,560 (GRCm39)	S118R	probably benign	Het
Vmn1r41	A	G	6: 89,724,080 (GRCm39)	Y207C	probably damaging	Het
Vmn2r79	A	G	7: 86,687,045 (GRCm39)	I809V	probably damaging	Het
Vnn1	G	A	10: 23,776,794 (GRCm39)	G382R	probably damaging	Het
Xcr1	A	T	9: 123,685,680 (GRCm39)	H27Q	probably benign	Het
Yeats2	T	A	16: 19,975,786 (GRCm39)	N94K	probably benign	Het
Zfp28	C	T	7: 6,397,440 (GRCm39)	T625M	probably damaging	Het
Zfp521	T	C	18: 13,977,698 (GRCm39)	Q905R	probably benign	Het
Zfp804b	T	C	5: 6,821,398 (GRCm39)	D555G	probably damaging	Het

Other mutations in Amt

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL02657:Amt	APN	9	108,178,579 (GRCm39)	missense	probably damaging	1.00
IGL03277:Amt	APN	9	108,178,418 (GRCm39)	missense	probably benign
R1333:Amt	UTSW	9	108,178,296 (GRCm39)	missense	probably benign	0.04
R1856:Amt	UTSW	9	108,174,361 (GRCm39)	missense	probably damaging	1.00
R3843:Amt	UTSW	9	108,174,420 (GRCm39)	missense	possibly damaging	0.74
R3844:Amt	UTSW	9	108,174,420 (GRCm39)	missense	possibly damaging	0.74
R3903:Amt	UTSW	9	108,174,420 (GRCm39)	missense	possibly damaging	0.74
R3904:Amt	UTSW	9	108,174,420 (GRCm39)	missense	possibly damaging	0.74
R4729:Amt	UTSW	9	108,177,851 (GRCm39)	missense	probably damaging	1.00
R4814:Amt	UTSW	9	108,176,979 (GRCm39)	missense	probably benign
R5149:Amt	UTSW	9	108,178,650 (GRCm39)	missense	possibly damaging	0.59
R6000:Amt	UTSW	9	108,178,684 (GRCm39)	missense	probably benign	0.20
R6044:Amt	UTSW	9	108,174,450 (GRCm39)	missense	probably damaging	1.00
R6911:Amt	UTSW	9	108,178,428 (GRCm39)	critical splice donor site	probably null
R6957:Amt	UTSW	9	108,177,032 (GRCm39)	missense	possibly damaging	0.51
R7618:Amt	UTSW	9	108,177,077 (GRCm39)	missense	probably damaging	1.00
R7658:Amt	UTSW	9	108,174,430 (GRCm39)	missense	probably damaging	0.98
R7783:Amt	UTSW	9	108,174,414 (GRCm39)	nonsense	probably null

Predicted Primers

PCR Primer
(F):5'- ACTATGGCTTACAGTCTGGTG -3'
(R):5'- TGGGCACAAAGGGCATTTTG -3'

Sequencing Primer
(F):5'- GTGTTATGTTCCAGGGAAGCGC -3'
(R):5'- CTGGTCGACTGTACTTAAATGGCAC -3'

Posted On

2022-03-25