Mutagenetix > Incidental Mutation

Incidental Mutation 'R6014:Shmt1'

479930

Institutional Source

Beutler Lab

Gene Symbol

Shmt1

Ensembl Gene

ENSMUSG00000020534

Gene Name

serine hydroxymethyltransferase 1 (soluble)

Synonyms

mshmt, mshmt2, mshmt1, Shmt

MMRRC Submission

044190-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R6014 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

60678933-60702091 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

C to A at 60688383 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Glycine to Valine at position 255 (G255V)

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: G255V

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000018744
Gene: ENSMUSG00000020534
AA Change: G255V

Domain	Start	End	E-Value	Type
Pfam:SHMT	20	419	1.3e-211	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: ENSMUST00000173698

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000174093

Predicted Effect

unknown
Transcript: ENSMUST00000174719
AA Change: G254V

SMART Domains

Protein: ENSMUSP00000134318
Gene: ENSMUSG00000020534
AA Change: G254V

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

Predicted Effect

unknown
Transcript: ENSMUST00000174214
AA Change: G254V

SMART Domains

Protein: ENSMUSP00000134269
Gene: ENSMUSG00000020534
AA Change: G254V

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

probably benign
Transcript: ENSMUST00000174174

SMART Domains

Protein: ENSMUSP00000134703
Gene: ENSMUSG00000020534

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

Meta Mutation Damage Score

0.9663

Coding Region Coverage

1x: 99.9%
3x: 99.5%
10x: 97.8%
20x: 93.3%

Validation Efficiency

100% (67/67)

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: 67 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4930568D16Rik	A	T	2: 35,244,881 (GRCm39)	M157K	probably benign	Het
A2ml1	C	T	6: 128,548,948 (GRCm39)	C278Y	probably damaging	Het
Abcc2	A	T	19: 43,815,174 (GRCm39)	Q1187L	probably benign	Het
Adcy9	A	T	16: 4,236,683 (GRCm39)	Y6N	probably damaging	Het
Adh1	T	C	3: 137,992,559 (GRCm39)	I225T	probably benign	Het
Akap11	A	T	14: 78,749,939 (GRCm39)	I816K	probably benign	Het
Ap1b1	T	A	11: 4,969,364 (GRCm39)	M240K	possibly damaging	Het
Apex1	A	T	14: 51,162,982 (GRCm39)	T17S	probably benign	Het
Arhgap21	C	T	2: 20,886,616 (GRCm39)	G26D	probably damaging	Het
Bahcc1	A	G	11: 120,180,615 (GRCm39)	Y2613C	probably benign	Het
Baz1b	C	T	5: 135,246,248 (GRCm39)	R566W	probably damaging	Het
Casp8ap2	A	T	4: 32,641,400 (GRCm39)	Y818F	probably damaging	Het
Col3a1	T	A	1: 45,360,739 (GRCm39)	C56*	probably null	Het
Coro2a	G	A	4: 46,542,261 (GRCm39)	P371S	probably damaging	Het
Cyp2a22	T	A	7: 26,638,605 (GRCm39)		probably null	Het
Dpysl3	T	A	18: 43,494,132 (GRCm39)	I183F	probably damaging	Het
Drc1	A	T	5: 30,502,993 (GRCm39)	N172I	probably damaging	Het
Dst	T	C	1: 34,303,915 (GRCm39)	Y1378H	probably damaging	Het
Dync2i2	C	T	2: 29,921,763 (GRCm39)	A533T	probably benign	Het
Eml2	G	A	7: 18,935,088 (GRCm39)	V432I	probably damaging	Het
Epb41l3	A	T	17: 69,590,955 (GRCm39)	T91S	probably damaging	Het
Exoc4	T	C	6: 33,452,932 (GRCm39)	V474A	probably benign	Het
Fam229b	G	A	10: 38,994,989 (GRCm39)	T56I	probably damaging	Het
Gfm2	A	G	13: 97,288,169 (GRCm39)		probably null	Het
Git2	C	T	5: 114,871,938 (GRCm39)	E152K	probably benign	Het
Golt1b	T	A	6: 142,341,943 (GRCm39)	I109N	probably damaging	Het
Grid2ip	T	A	5: 143,373,578 (GRCm39)	M783K	possibly damaging	Het
Inpp5a	A	G	7: 139,154,898 (GRCm39)	Y339C	probably damaging	Het
Isoc2a	T	C	7: 4,894,625 (GRCm39)	S103P	probably damaging	Het
Itih4	C	A	14: 30,614,586 (GRCm39)	Q483K	probably benign	Het
Kansl2	A	G	15: 98,418,197 (GRCm39)		probably null	Het
Kdm5d	G	A	Y: 921,528 (GRCm39)	A509T	probably benign	Het
Krt13	A	T	11: 100,008,437 (GRCm39)	D433E	unknown	Het
Lat2	C	T	5: 134,632,308 (GRCm39)	V142M	probably damaging	Het
Lemd1	A	C	1: 132,184,463 (GRCm39)	*102S	probably null	Het
Lrfn2	T	C	17: 49,376,934 (GRCm39)	L5P	possibly damaging	Het
Lrrc4c	T	G	2: 97,459,557 (GRCm39)		probably null	Het
Lypla1	T	A	1: 4,878,594 (GRCm39)		probably null	Het
Magi2	G	A	5: 20,816,091 (GRCm39)	G744R	probably damaging	Het
Myh14	T	A	7: 44,274,502 (GRCm39)	E948V	probably null	Het
Myo5a	C	A	9: 75,074,489 (GRCm39)	Y799*	probably null	Het
Nacc1	A	C	8: 85,401,700 (GRCm39)	M371R	possibly damaging	Het
Nlrp5	T	G	7: 23,109,372 (GRCm39)	M106R	probably benign	Het
Oas1h	C	T	5: 121,005,229 (GRCm39)	H226Y	possibly damaging	Het
Obscn	A	C	11: 58,929,690 (GRCm39)	I5175R	probably damaging	Het
Pcdh7	T	A	5: 57,878,497 (GRCm39)	I684N	probably damaging	Het
Pcdhb3	T	A	18: 37,435,706 (GRCm39)	N557K	probably damaging	Het
Pde3b	T	C	7: 114,015,675 (GRCm39)	L297S	probably damaging	Het
Pigv	G	T	4: 133,392,740 (GRCm39)	H143Q	probably benign	Het
Ptk2	T	G	15: 73,176,293 (GRCm39)	Y251S	possibly damaging	Het
Ralgds	A	G	2: 28,433,673 (GRCm39)	N219S	probably damaging	Het
Sardh	C	A	2: 27,087,540 (GRCm39)		probably null	Het
Serpina3b	A	T	12: 104,097,356 (GRCm39)	K212N	possibly damaging	Het
Sh3bp2	A	G	5: 34,716,971 (GRCm39)	N461D	probably benign	Het
Shisa2	A	T	14: 59,867,357 (GRCm39)	Q203L	probably damaging	Het
Socs1	T	A	16: 10,602,357 (GRCm39)	I127F	possibly damaging	Het
Srcap	A	T	7: 127,137,922 (GRCm39)	T1091S	probably benign	Het
Syt14	A	G	1: 192,613,003 (GRCm39)	I599T	probably damaging	Het
Tep1	A	T	14: 51,084,457 (GRCm39)	N907K	probably benign	Het
Themis2	A	G	4: 132,513,291 (GRCm39)	Y312H	probably benign	Het
Tubgcp5	T	G	7: 55,473,357 (GRCm39)	S812A	probably benign	Het
Ush2a	A	T	1: 188,582,237 (GRCm39)	I3767F	probably damaging	Het
Usp40	T	A	1: 87,907,738 (GRCm39)	E626V	probably damaging	Het
Utrn	T	C	10: 12,566,620 (GRCm39)	R1181G	probably benign	Het
Vmn2r117	T	A	17: 23,698,535 (GRCm39)	I13F	probably damaging	Het
Wdr48	G	T	9: 119,753,775 (GRCm39)	V646F	probably damaging	Het
Wdr64	T	C	1: 175,633,556 (GRCm39)	F936L	possibly damaging	Het

Other mutations in Shmt1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL02088:Shmt1	APN	11	60,680,479 (GRCm39)	missense	probably damaging	1.00
PIT4514001:Shmt1	UTSW	11	60,695,173 (GRCm39)	missense	probably damaging	1.00
R0470:Shmt1	UTSW	11	60,683,789 (GRCm39)	missense	possibly damaging	0.91
R0787:Shmt1	UTSW	11	60,683,802 (GRCm39)	missense	probably benign	0.00
R1768:Shmt1	UTSW	11	60,683,790 (GRCm39)	missense	probably damaging	1.00
R2179:Shmt1	UTSW	11	60,697,825 (GRCm39)	missense	possibly damaging	0.69
R3715:Shmt1	UTSW	11	60,688,402 (GRCm39)	missense	probably damaging	1.00
R4647:Shmt1	UTSW	11	60,692,291 (GRCm39)	missense	probably damaging	1.00
R5024:Shmt1	UTSW	11	60,688,305 (GRCm39)	intron	probably benign
R5183:Shmt1	UTSW	11	60,688,308 (GRCm39)	intron	probably benign
R5461:Shmt1	UTSW	11	60,685,725 (GRCm39)	missense	possibly damaging	0.94
R6618:Shmt1	UTSW	11	60,683,772 (GRCm39)	splice site	probably null
R6969:Shmt1	UTSW	11	60,695,153 (GRCm39)	missense	probably damaging	1.00
R7108:Shmt1	UTSW	11	60,689,470 (GRCm39)	missense	probably damaging	0.98
R7158:Shmt1	UTSW	11	60,681,068 (GRCm39)	missense	probably benign	0.03
R7215:Shmt1	UTSW	11	60,692,361 (GRCm39)	missense	probably damaging	0.99
R7514:Shmt1	UTSW	11	60,692,812 (GRCm39)	missense	probably damaging	1.00
R8717:Shmt1	UTSW	11	60,685,763 (GRCm39)	missense	probably benign	0.00
R9673:Shmt1	UTSW	11	60,692,769 (GRCm39)	missense	probably damaging	1.00
R9781:Shmt1	UTSW	11	60,692,329 (GRCm39)	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- ACTGTTATTTCTTCCTGAGGAGC -3'
(R):5'- TGTACTCTCAGAGGCCAACTC -3'

Sequencing Primer
(F):5'- AGCTCTTCCAAGGCCAGAG -3'
(R):5'- CTGGGGATCTTTGACACTACCATG -3'

Posted On

2017-06-26