Mutagenetix > Incidental Mutation

Incidental Mutation 'R6000:Amt'

480788

Institutional Source

Beutler Lab

Gene Symbol

Amt

Ensembl Gene

ENSMUSG00000032607

Gene Name

aminomethyltransferase

Synonyms

EG434437

MMRRC Submission

044179-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R6000 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

108174104-108179501 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to T at 108178684 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Tyrosine to Phenylalanine at position 400 (Y400F)

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: Y400F

PolyPhen 2 Score 0.202 (Sensitivity: 0.92; Specificity: 0.88)

SMART Domains

Protein: ENSMUSP00000035230
Gene: ENSMUSG00000032607
AA Change: Y400F

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

noncoding transcript
Transcript: ENSMUST00000160025

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000160675

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000162568

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000193619

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: 99.9%
3x: 99.5%
10x: 97.4%
20x: 91.7%

Validation Efficiency

100% (64/64)

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: 66 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
2310034C09Rik	T	C	16: 88,556,427 (GRCm39)	C214R	possibly damaging	Het
Ahnak	A	T	19: 8,990,475 (GRCm39)	K3920*	probably null	Het
Alox12b	A	G	11: 69,060,394 (GRCm39)	D650G	probably damaging	Het
Ankrd11	A	G	8: 123,617,934 (GRCm39)	S1973P	possibly damaging	Het
Aoc1	A	T	6: 48,884,573 (GRCm39)	T539S	probably benign	Het
Arhgap44	CTGCT	CTGCTTGCT	11: 64,922,910 (GRCm39)		probably null	Het
Ccdc15	C	T	9: 37,227,060 (GRCm39)	G292S	probably benign	Het
Ccdc162	C	T	10: 41,437,159 (GRCm39)	C287Y	possibly damaging	Het
Ccn6	T	C	10: 39,034,296 (GRCm39)	Y102C	probably damaging	Het
Cdk15	G	A	1: 59,328,818 (GRCm39)	G244D	probably damaging	Het
Cep290	T	A	10: 100,377,649 (GRCm39)	Y1560N	probably damaging	Het
Cfap251	A	G	5: 123,392,435 (GRCm39)		probably benign	Het
Cic	A	C	7: 24,971,423 (GRCm39)	I385L	probably benign	Het
Cobl	A	T	11: 12,319,684 (GRCm39)	F231L	probably benign	Het
Cpeb1	T	C	7: 81,011,428 (GRCm39)	D171G	possibly damaging	Het
Csnk1g2	T	A	10: 80,474,778 (GRCm39)	V305E	probably damaging	Het
Cyp2c29	A	G	19: 39,296,050 (GRCm39)		probably null	Het
Dner	A	T	1: 84,361,650 (GRCm39)	M653K	possibly damaging	Het
Dst	T	A	1: 34,251,304 (GRCm39)	M4311K	possibly damaging	Het
Ep400	A	G	5: 110,831,067 (GRCm39)	S2200P	unknown	Het
Ephb2	A	T	4: 136,411,341 (GRCm39)	S440T	possibly damaging	Het
Ercc1	A	T	7: 19,081,086 (GRCm39)		probably benign	Het
Folh1	T	A	7: 86,375,142 (GRCm39)	N615Y	probably benign	Het
Gm7298	T	C	6: 121,742,038 (GRCm39)	Y487H	possibly damaging	Het
Gucy1b2	A	T	14: 62,656,499 (GRCm39)	I286N	probably benign	Het
Hr	A	G	14: 70,805,273 (GRCm39)	D1005G	probably damaging	Het
Ifrd1	C	A	12: 40,266,243 (GRCm39)	V117F	possibly damaging	Het
Ift140	A	T	17: 25,255,934 (GRCm39)	T210S	probably benign	Het
Igll1	C	A	16: 16,681,805 (GRCm39)		probably benign	Het
Ino80	G	T	2: 119,204,989 (GRCm39)	S1512R	probably benign	Het
Intu	A	T	3: 40,608,578 (GRCm39)	K197*	probably null	Het
Kdm6b	A	G	11: 69,294,424 (GRCm39)	L1216P	unknown	Het
Klrb1c	T	G	6: 128,761,120 (GRCm39)	D169A	probably damaging	Het
Lamp3	T	A	16: 19,519,698 (GRCm39)	T162S	possibly damaging	Het
Mapk10	G	A	5: 103,114,342 (GRCm39)	P319S	probably damaging	Het
Mapk10	G	A	5: 103,114,341 (GRCm39)	P319L	probably damaging	Het
Mical3	T	C	6: 120,998,281 (GRCm39)	T702A	probably benign	Het
Mstn	C	T	1: 53,100,828 (GRCm39)		probably benign	Het
Nckap1l	T	C	15: 103,387,242 (GRCm39)	S706P	probably benign	Het
Nckap5l	G	A	15: 99,324,766 (GRCm39)	T579I	probably damaging	Het
Or13p3	A	T	4: 118,567,441 (GRCm39)	N279I	probably damaging	Het
Or4a27	C	A	2: 88,559,575 (GRCm39)	A123S	probably damaging	Het
Or8s16	G	A	15: 98,211,317 (GRCm39)	T38I	probably benign	Het
Pcdh18	A	C	3: 49,708,913 (GRCm39)	S801A	probably damaging	Het
Pde11a	A	T	2: 75,848,204 (GRCm39)	D874E	probably damaging	Het
Pfdn6	G	T	17: 34,158,589 (GRCm39)	P62T	probably damaging	Het
Pkd1l1	A	G	11: 8,900,427 (GRCm39)	I38T	probably benign	Het
Prkdc	A	T	16: 15,647,561 (GRCm39)	I3662F	possibly damaging	Het
Psg26	A	T	7: 18,216,617 (GRCm39)	L74*	probably null	Het
Rassf6	A	G	5: 90,751,736 (GRCm39)	V341A	probably damaging	Het
Rsad2	C	A	12: 26,497,150 (GRCm39)		probably null	Het
Rwdd3	A	G	3: 120,950,162 (GRCm39)	Y95H	probably damaging	Het
Scfd1	A	G	12: 51,492,457 (GRCm39)	I589V	possibly damaging	Het
Sgsm1	A	T	5: 113,434,704 (GRCm39)	I131N	probably damaging	Het
Tecpr1	A	G	5: 144,148,239 (GRCm39)	S389P	probably benign	Het
Tle3	T	A	9: 61,281,296 (GRCm39)	I29N	probably damaging	Het
Tmem63c	C	A	12: 87,103,971 (GRCm39)	N73K	probably damaging	Het
Tpm2	T	A	4: 43,518,301 (GRCm39)		probably null	Het
Trak2	A	T	1: 58,950,971 (GRCm39)	D405E	possibly damaging	Het
Ttn	C	A	2: 76,575,516 (GRCm39)	A23380S	probably damaging	Het
Ttn	A	T	2: 76,715,495 (GRCm39)		probably benign	Het
Tub	T	C	7: 108,628,857 (GRCm39)	S391P	probably damaging	Het
Ush2a	G	T	1: 187,999,223 (GRCm39)	E178*	probably null	Het
Vamp9	G	T	5: 100,089,226 (GRCm39)	A164S	probably benign	Het
Ylpm1	C	A	12: 85,044,030 (GRCm39)	T256K	unknown	Het
Zfp1007	A	G	5: 109,824,730 (GRCm39)	V240A	probably benign	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
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
R9276:Amt	UTSW	9	108,178,410 (GRCm39)	missense	probably benign	0.00

Predicted Primers

PCR Primer
(F):5'- TGGTGCTAACTTATGGCCTATGC -3'
(R):5'- TGGGCCCTAAAATTGGAATGGC -3'

Sequencing Primer
(F):5'- CGATGGGTTATGTGCCAT -3'
(R):5'- CCCTAAAATTGGAATGGCTTGTAAGG -3'

Posted On

2017-06-26