Mutagenetix > Incidental Mutation

Incidental Mutation 'R7215:Shmt1'

561402

Institutional Source

Beutler Lab

Gene Symbol

Shmt1

Ensembl Gene

ENSMUSG00000020534

Gene Name

serine hydroxymethyltransferase 1 (soluble)

Synonyms

mshmt1, Shmt, mshmt2, mshmt

MMRRC Submission

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R7215 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

60788104-60811718 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 60801535 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Isoleucine to Valine at position 132 (I132V)

Ref Sequence

ENSEMBL: ENSMUSP00000018744 (fasta)

Gene Model

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

AlphaFold

P50431

PDB Structure

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

Predicted Effect

probably damaging
Transcript: ENSMUST00000018744
AA Change: I132V

PolyPhen 2 Score 0.994 (Sensitivity: 0.69; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000018744
Gene: ENSMUSG00000020534
AA Change: I132V

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

Predicted Effect

SMART Domains

Protein: ENSMUSP00000134703
Gene: ENSMUSG00000020534
AA Change: N92S

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

Predicted Effect

SMART Domains

Protein: ENSMUSP00000134269
Gene: ENSMUSG00000020534
AA Change: I131V

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

SMART Domains

Protein: ENSMUSP00000134318
Gene: ENSMUSG00000020534
AA Change: I131V

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

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.6%
20x: 98.8%

Validation Efficiency

98% (79/81)

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: 82 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
2210408I21Rik	G	A	13: 77,323,571	V1032M	possibly damaging	Het
Abca13	T	A	11: 9,288,405		probably null	Het
Adamts14	T	A	10: 61,211,596	H739L	possibly damaging	Het
Adgrl3	A	G	5: 81,693,550	E758G	probably damaging	Het
Ano3	T	A	2: 110,665,932	T826S	probably damaging	Het
Arhgap45	C	T	10: 80,025,482	T493I	possibly damaging	Het
Atg9b	A	C	5: 24,388,041	W455G	probably damaging	Het
Atp4a	A	G	7: 30,717,360	N496S	possibly damaging	Het
Bckdk	T	A	7: 127,905,110	D60E	possibly damaging	Het
Blmh	A	T	11: 76,965,899	K244*	probably null	Het
Btbd17	T	C	11: 114,791,465	I474V	possibly damaging	Het
C87436	A	G	6: 86,462,680	E451G	possibly damaging	Het
Camta1	T	C	4: 151,144,737	E546G	probably damaging	Het
Casp1	A	G	9: 5,298,523		probably null	Het
Ccdc114	C	T	7: 45,936,622	R148C	probably damaging	Het
Ccdc116	A	G	16: 17,139,928	Y456H	probably damaging	Het
Cep350	A	C	1: 155,894,707	S1812R	possibly damaging	Het
Chrna10	A	G	7: 102,112,208	L392P	possibly damaging	Het
Col22a1	A	T	15: 71,970,332	C434*	probably null	Het
Cxcl9	G	A	5: 92,323,888	Q98*	probably null	Het
Cyp2c54	G	A	19: 40,046,182	T348I	probably damaging	Het
Dnah7a	G	A	1: 53,618,350	R756C	probably damaging	Het
Dnajc18	T	C	18: 35,681,981	T239A	probably benign	Het
Dnase2a	A	T	8: 84,909,770		probably null	Het
Dpyd	A	G	3: 119,266,032	T793A	probably benign	Het
E430018J23Rik	A	G	7: 127,391,523	S431P	probably benign	Het
Edil3	T	C	13: 88,822,050		probably null	Het
Ehd1	T	A	19: 6,297,642	I342N	possibly damaging	Het
Erbb4	A	T	1: 68,339,460	S341T	probably benign	Het
Ezh1	T	A	11: 101,215,299	T87S	probably benign	Het
Fam20b	A	T	1: 156,690,553	W224R	probably damaging	Het
Galns	A	T	8: 122,599,348		probably null	Het
Gm13283	C	T	4: 88,760,730		probably benign	Het
Gm15448	C	T	7: 3,822,311	C444Y	unknown	Het
Gm49342	A	T	14: 50,944,583	M23L	probably benign	Het
Gm5114	T	A	7: 39,411,371	H18L	probably benign	Het
Gpr89	A	G	3: 96,880,088	W299R	probably damaging	Het
Hadha	G	T	5: 30,119,842	N755K	probably benign	Het
Inpp5d	A	T	1: 87,701,218	H620L	probably benign	Het
Klk1b3	T	A	7: 44,200,404		probably null	Het
Macf1	T	C	4: 123,507,304	T663A	probably damaging	Het
Man1b1	A	G	2: 25,350,390	N601S	probably benign	Het
Mbtps1	A	G	8: 119,524,568	V605A	possibly damaging	Het
Med23	C	G	10: 24,888,429	D311E	probably benign	Het
Myo3a	G	T	2: 22,245,567	D82Y	possibly damaging	Het
Nsd1	T	A	13: 55,247,641	D1121E	probably benign	Het
Olfr1042	C	T	2: 86,159,456	V305I	probably benign	Het
Olfr1221	G	A	2: 89,112,501	Q4*	probably null	Het
Olfr918	A	G	9: 38,673,447	I12T	probably benign	Het
Otoa	T	C	7: 121,118,572	V19A	unknown	Het
Pcdhb20	A	T	18: 37,505,386	T322S	probably benign	Het
Pecam1	T	C	11: 106,695,919	T257A	probably benign	Het
Pi16	G	T	17: 29,319,098		probably benign	Het
Pik3c2g	C	T	6: 139,754,863	T293M		Het
Pkhd1l1	T	A	15: 44,528,163	C1542S	possibly damaging	Het
Prrc2b	G	A	2: 32,229,297	G2172R	probably damaging	Het
Prrt1	A	T	17: 34,629,703		probably null	Het
Ptprb	T	A	10: 116,338,776	N784K	possibly damaging	Het
Rem1	C	A	2: 152,628,149	S18R	probably damaging	Het
Ripk4	G	A	16: 97,747,323		probably null	Het
Scn8a	G	A	15: 101,029,830	V1397I	possibly damaging	Het
Setbp1	T	A	18: 78,856,837	H1205L	probably damaging	Het
Slc24a1	T	A	9: 64,928,503	T781S	unknown	Het
Sncaip	C	T	18: 52,907,343	Q870*	probably null	Het
Stab1	A	T	14: 31,160,797	N416K	possibly damaging	Het
Tcea1	A	G	1: 4,867,483	D26G	probably damaging	Het
Tcf20	A	T	15: 82,853,489	S1254T	probably benign	Het
Tead4	T	A	6: 128,228,678	I354F	probably damaging	Het
Tex36	G	A	7: 133,587,418	R142*	probably null	Het
Trav6d-3	T	A	14: 52,725,342	L12Q	probably damaging	Het
Trpc4	A	G	3: 54,194,896	T72A	possibly damaging	Het
Trrap	G	A	5: 144,797,135	A933T	probably benign	Het
Tspoap1	T	A	11: 87,770,489	I589N	probably benign	Het
Ttll5	T	A	12: 85,933,396	V918E	probably benign	Het
Txn2	A	G	15: 77,927,686		probably null	Het
Ucn3	T	G	13: 3,941,365	T96P	probably benign	Het
Usp36	T	C	11: 118,265,154	E764G	possibly damaging	Het
Vmn2r23	A	T	6: 123,704,364	H77L	probably benign	Het
Vmn2r57	T	C	7: 41,400,286	T680A	probably benign	Het
Vwa3a	T	C	7: 120,795,630	I891T	possibly damaging	Het
Zcchc11	T	C	4: 108,527,008	Y1091H	probably damaging	Het
Zhx2	A	G	15: 57,823,643	I803V	probably benign	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
R0787:Shmt1	UTSW	11	60792976	missense	probably benign	0.00
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
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'- TGCTGAGTTACATCCCCAAC -3'
(R):5'- ACAGGGTGACTTTCTAAAGCTC -3'

Sequencing Primer
(F):5'- TGTTCATACAGAAGAGCCCCGAG -3'
(R):5'- GGTGACTTTCTAAAGCTCAGGAG -3'

Posted On

2019-06-26