Mutagenetix > Incidental Mutation

Incidental Mutation 'R0787:Shmt1'

76911

Institutional Source

Beutler Lab

Gene Symbol

Shmt1

Ensembl Gene

ENSMUSG00000020534

Gene Name

serine hydroxymethyltransferase 1 (soluble)

Synonyms

mshmt1, Shmt, mshmt2, mshmt

MMRRC Submission

038967-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R0787 (G1)

Quality Score

208

Status

Validated

Chromosome

Chromosomal Location

60788104-60811718 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 60792976 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Threonine to Alanine at position 337 (T337A)

Ref Sequence

ENSEMBL: ENSMUSP00000018744 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000018744] [ENSMUST00000056907]

AlphaFold

P50431

PDB Structure

RECOMBINANT SERINE HYDROXYMETHYLTRANSFERASE (MOUSE) [X-RAY DIFFRACTION]

Predicted Effect

probably benign
Transcript: ENSMUST00000018744
AA Change: T337A

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

SMART Domains

Protein: ENSMUSP00000018744
Gene: ENSMUSG00000020534
AA Change: T337A

Domain	Start	End	E-Value	Type
Pfam:SHMT	20	419	1.3e-211	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000056907

SMART Domains

Protein: ENSMUSP00000055926
Gene: ENSMUSG00000049323

Domain	Start	End	E-Value	Type
low complexity region	13	30	N/A	INTRINSIC
Pfam:Folliculin	78	262	5e-12	PFAM

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000124227

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000135081

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000172804

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000173260

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000174093

Predicted Effect

probably benign
Transcript: ENSMUST00000174174

SMART Domains

Protein: ENSMUSP00000134703
Gene: ENSMUSG00000020534

Domain	Start	End	E-Value	Type
Pfam:SHMT	20	79	7.1e-26	PFAM

Predicted Effect

unknown
Transcript: ENSMUST00000174214
AA Change: T336A

SMART Domains

Protein: ENSMUSP00000134269
Gene: ENSMUSG00000020534
AA Change: T336A

Domain	Start	End	E-Value	Type
Pfam:SHMT	20	408	4.6e-196	PFAM
Pfam:Aminotran_1_2	153	409	3.1e-6	PFAM

Predicted Effect

unknown
Transcript: ENSMUST00000174719
AA Change: T297A

SMART Domains

Protein: ENSMUSP00000134318
Gene: ENSMUSG00000020534
AA Change: T297A

Domain	Start	End	E-Value	Type
Pfam:SHMT	20	268	6.4e-137	PFAM
Pfam:SHMT	265	380	3.9e-51	PFAM

Meta Mutation Damage Score

0.0785

Coding Region Coverage

1x: 99.3%
3x: 98.7%
10x: 96.9%
20x: 93.4%

Validation Efficiency

100% (56/56)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes the cytosolic form of serine hydroxymethyltransferase, a pyridoxal phosphate-containing enzyme that catalyzes the reversible conversion of serine and tetrahydrofolate to glycine and 5,10-methylene tetrahydrofolate. This reaction provides one-carbon units for synthesis of methionine, thymidylate, and purines in the cytoplasm. This gene is located within the Smith-Magenis syndrome region on chromosome 17. A pseudogene of this gene is located on the short arm of chromosome 1. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2013]
PHENOTYPE: Mice with deficiencies in this gene display abnormalities in hepatic partioning of methylenetetrahydrofolate but are otherwise healthy and fertile. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 54 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
0610037L13Rik	T	A	4: 107,890,129	L6Q	probably damaging	Het
1700001F09Rik	A	T	14: 43,345,493		probably null	Het
Abca8a	T	A	11: 110,042,988	Y1197F	possibly damaging	Het
Abcc2	T	C	19: 43,798,516		probably null	Het
Adamts16	A	T	13: 70,738,829	C979S	probably damaging	Het
Agap2	T	A	10: 127,085,150	D523E	unknown	Het
Ankfy1	T	A	11: 72,760,296	I1024N	probably damaging	Het
Ankrd13c	A	G	3: 157,994,678	S379G	probably null	Het
Arhgap40	T	C	2: 158,547,790	S625P	probably benign	Het
Armc12	G	C	17: 28,538,766	A291P	probably damaging	Het
Armc9	A	G	1: 86,202,505	N524D	probably damaging	Het
Col12a1	G	T	9: 79,638,485	T2305K	probably damaging	Het
Cyp2c54	T	C	19: 40,047,635	N277S	probably benign	Het
E130311K13Rik	A	T	3: 63,920,298	V129E	probably benign	Het
Ehbp1l1	T	C	19: 5,722,668	D79G	possibly damaging	Het
Epb41l1	A	G	2: 156,494,090	E58G	probably damaging	Het
Fam217b	T	A	2: 178,420,909	V222E	probably benign	Het
Fat1	T	A	8: 45,040,555	Y3913N	probably damaging	Het
Fgd4	A	G	16: 16,423,901		probably benign	Het
Hltf	A	T	3: 20,106,446	D759V	probably damaging	Het
Hsp90ab1	ACTTCTT	ACTT	17: 45,569,499		probably benign	Het
Isg15	C	T	4: 156,199,939	R44H	probably benign	Het
Itga4	C	T	2: 79,279,153	T232I	probably benign	Het
Kntc1	C	A	5: 123,796,104	H1399Q	probably benign	Het
Lig1	A	C	7: 13,299,069	K499Q	probably benign	Het
Lrrn3	C	A	12: 41,454,231	C29F	probably damaging	Het
Mtmr10	T	C	7: 64,300,615	I136T	possibly damaging	Het
Naip1	A	G	13: 100,426,096	Y854H	probably benign	Het
Olfr770	T	C	10: 129,133,526	N81D	possibly damaging	Het
Pcdh9	G	A	14: 93,886,757	A659V	possibly damaging	Het
Phf20l1	T	A	15: 66,615,630		probably benign	Het
Phgdh	A	G	3: 98,334,549	V83A	probably damaging	Het
Pik3r1	A	T	13: 101,690,523	M326K	probably benign	Het
Pirb	A	T	7: 3,717,638	L287Q	probably benign	Het
Pkd1l2	T	C	8: 117,076,177	D235G	possibly damaging	Het
Pkhd1l1	C	A	15: 44,529,264	P1665Q	probably damaging	Het
Ppp1r7	A	G	1: 93,364,956	T326A	probably damaging	Het
Prr22	A	T	17: 56,771,072	Y75F	possibly damaging	Het
Ptov1	A	C	7: 44,865,470		probably null	Het
Rasal2	A	G	1: 157,158,696	S766P	probably damaging	Het
St5	G	T	7: 109,525,620	R1068S	possibly damaging	Het
Tbc1d4	A	T	14: 101,449,209	I1168N	probably damaging	Het
Tecpr2	T	C	12: 110,946,343	V1126A	probably benign	Het
Tep1	A	T	14: 50,829,230	S2304T	possibly damaging	Het
Tiam1	C	A	16: 89,789,561	R1446M	probably damaging	Het
Tmem87a	T	C	2: 120,370,484	I425V	probably benign	Het
Ubr3	T	C	2: 69,951,421		probably benign	Het
Ubxn7	T	A	16: 32,381,763		probably benign	Het
Vmn2r13	A	G	5: 109,156,847	S573P	probably damaging	Het
Wdfy3	A	T	5: 101,957,388	V191E	probably damaging	Het
Zdhhc3	A	T	9: 123,083,623	C153*	probably null	Het
Zfp407	A	T	18: 84,209,022	V2154D	probably damaging	Het
Zfp407	A	G	18: 84,209,346	V2046A	probably benign	Het
Zfr	T	A	15: 12,140,548	I227N	unknown	Het

Other mutations in Shmt1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL02088:Shmt1	APN	11	60789653	missense	probably damaging	1.00
PIT4514001:Shmt1	UTSW	11	60804347	missense	probably damaging	1.00
R0470:Shmt1	UTSW	11	60792963	missense	possibly damaging	0.91
R1768:Shmt1	UTSW	11	60792964	missense	probably damaging	1.00
R2179:Shmt1	UTSW	11	60806999	missense	possibly damaging	0.69
R3715:Shmt1	UTSW	11	60797576	missense	probably damaging	1.00
R4647:Shmt1	UTSW	11	60801465	missense	probably damaging	1.00
R5024:Shmt1	UTSW	11	60797479	intron	probably benign
R5183:Shmt1	UTSW	11	60797482	intron	probably benign
R5461:Shmt1	UTSW	11	60794899	missense	possibly damaging	0.94
R6014:Shmt1	UTSW	11	60797557	missense	probably damaging	1.00
R6618:Shmt1	UTSW	11	60792946	splice site	probably null
R6969:Shmt1	UTSW	11	60804327	missense	probably damaging	1.00
R7108:Shmt1	UTSW	11	60798644	missense	probably damaging	0.98
R7158:Shmt1	UTSW	11	60790242	missense	probably benign	0.03
R7215:Shmt1	UTSW	11	60801535	missense	probably damaging	0.99
R7514:Shmt1	UTSW	11	60801986	missense	probably damaging	1.00
R8717:Shmt1	UTSW	11	60794937	missense	probably benign	0.00
R9673:Shmt1	UTSW	11	60801943	missense	probably damaging	1.00
R9781:Shmt1	UTSW	11	60801503	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- TCCATGTTGGGTGTCAAATGGAAGC -3'
(R):5'- GTGGTAATCGGATAACCACTGGGC -3'

Sequencing Primer
(F):5'- GGTGTCAAATGGAAGCTACTTG -3'
(R):5'- gggtggcagggtagttaag -3'

Posted On

2013-10-16