Mutagenetix > Incidental Mutation

Incidental Mutation 'R5024:Shmt1'

391249

Institutional Source

Beutler Lab

Gene Symbol

Shmt1

Ensembl Gene

ENSMUSG00000020534

Gene Name

serine hydroxymethyltransferase 1 (soluble)

Synonyms

mshmt, mshmt2, mshmt1, Shmt

MMRRC Submission

042615-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R5024 (G1)

Quality Score

210

Status

Validated

Chromosome

Chromosomal Location

60678933-60702091 bp(-) (GRCm39)

Type of Mutation

intron

DNA Base Change (assembly)

A to T at 60688305 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Gene Model

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

AlphaFold

P50431

Predicted Effect

probably benign
Transcript: ENSMUST00000018744

SMART Domains

Protein: ENSMUSP00000018744
Gene: ENSMUSG00000020534

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

probably benign
Transcript: ENSMUST00000174214

SMART Domains

Protein: ENSMUSP00000134269
Gene: ENSMUSG00000020534

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: ENSMUST00000174719

SMART Domains

Protein: ENSMUSP00000134318
Gene: ENSMUSG00000020534

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

0.0898

Coding Region Coverage

1x: 99.2%
3x: 98.4%
10x: 96.6%
20x: 93.4%

Validation Efficiency

99% (95/96)

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: 85 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Adgrd1	A	G	5: 129,248,959 (GRCm39)	N575S	probably damaging	Het
Akap6	C	T	12: 53,189,345 (GRCm39)	T2253M	probably benign	Het
Arhgef37	A	C	18: 61,639,511 (GRCm39)	N289K	probably damaging	Het
Atad2b	A	C	12: 4,987,534 (GRCm39)	T121P	probably benign	Het
Atp4a	A	C	7: 30,415,289 (GRCm39)	D303A	possibly damaging	Het
Calu	A	T	6: 29,374,518 (GRCm39)		probably benign	Het
Ccdc141	A	C	2: 76,885,047 (GRCm39)	N531K	probably benign	Het
Ccdc146	T	C	5: 21,604,612 (GRCm39)		probably null	Het
Cd207	G	A	6: 83,651,301 (GRCm39)	T218I	probably damaging	Het
Cd2ap	A	C	17: 43,116,236 (GRCm39)		probably null	Het
Ceacam23	A	G	7: 17,644,607 (GRCm39)	I575V	probably benign	Het
Clip3	G	A	7: 29,991,644 (GRCm39)		probably benign	Het
Clstn1	G	A	4: 149,719,751 (GRCm39)	R432H	possibly damaging	Het
Csmd2	A	G	4: 128,215,141 (GRCm39)	Y521C	possibly damaging	Het
Dnah8	A	T	17: 30,955,070 (GRCm39)	E2033V	probably damaging	Het
Eng	T	G	2: 32,563,404 (GRCm39)	V319G	probably benign	Het
Erp44	C	T	4: 48,241,296 (GRCm39)	W57*	probably null	Het
Etv1	T	A	12: 38,904,233 (GRCm39)		probably null	Het
Eva1c	T	C	16: 90,673,081 (GRCm39)		probably null	Het
Fam221b	T	A	4: 43,659,674 (GRCm39)	N482I	probably damaging	Het
Fam83h	T	C	15: 75,876,991 (GRCm39)	H202R	probably damaging	Het
Fbxw13	T	C	9: 109,008,403 (GRCm39)	T449A	probably benign	Het
Fbxw25	A	T	9: 109,492,442 (GRCm39)		probably null	Het
Frmd3	T	A	4: 74,016,381 (GRCm39)	S99T	probably benign	Het
Gm5174	G	T	10: 86,492,451 (GRCm39)		noncoding transcript	Het
Gm815	C	T	19: 26,865,175 (GRCm39)	Q49*	probably null	Het
H2-DMa	A	T	17: 34,357,461 (GRCm39)	I245F	possibly damaging	Het
Herc1	A	T	9: 66,377,608 (GRCm39)	K3458M	possibly damaging	Het
Hirip3	A	G	7: 126,463,661 (GRCm39)		probably null	Het
Hjurp	A	T	1: 88,202,772 (GRCm39)	Y71N	possibly damaging	Het
Hmcn1	T	A	1: 150,556,439 (GRCm39)	E2449V	possibly damaging	Het
Igll1	G	T	16: 16,681,657 (GRCm39)	H33N	probably benign	Het
Il6	T	C	5: 30,224,512 (GRCm39)	L184P	probably damaging	Het
Impg2	T	A	16: 56,080,463 (GRCm39)	S756T	probably damaging	Het
Insyn2a	A	G	7: 134,520,207 (GRCm39)	S108P	probably damaging	Het
Kank4	T	G	4: 98,673,898 (GRCm39)	D5A	probably damaging	Het
Kcna7	G	A	7: 45,056,015 (GRCm39)	R77H	probably damaging	Het
Kcns2	A	T	15: 34,839,683 (GRCm39)	T349S	probably benign	Het
Keap1	A	G	9: 21,148,522 (GRCm39)	Y162H	probably damaging	Het
Kif9	T	C	9: 110,312,161 (GRCm39)	F10L	possibly damaging	Het
Klhdc8b	ACACGCACGCACGCACGCACGCACGCACGCACGCACGCAC	ACACGCACGCACGCACGCACGCACGCACGCACGCACGCACGCAC	9: 108,326,184 (GRCm39)		probably benign	Het
Klk14	G	A	7: 43,341,501 (GRCm39)	C51Y	probably damaging	Het
Lpar6	A	G	14: 73,476,809 (GRCm39)	T257A	probably damaging	Het
Lpin1	A	T	12: 16,604,007 (GRCm39)	L608Q	probably benign	Het
Lyst	T	C	13: 13,808,989 (GRCm39)	S220P	probably benign	Het
M1ap	A	G	6: 83,005,339 (GRCm39)		probably benign	Het
Mbd6	C	T	10: 127,122,310 (GRCm39)	V173I	probably benign	Het
Myo5b	A	T	18: 74,849,105 (GRCm39)	T1115S	possibly damaging	Het
Mysm1	C	A	4: 94,839,253 (GRCm39)	V683F	possibly damaging	Het
Nlrp4g	T	A	9: 124,350,155 (GRCm38)		noncoding transcript	Het
Odad2	T	C	18: 7,088,555 (GRCm39)	M1005V	probably benign	Het
Or14c39	A	T	7: 86,344,089 (GRCm39)	M142L	probably benign	Het
Or2ak5	T	A	11: 58,611,776 (GRCm39)	I33F	probably benign	Het
Or5al6	G	T	2: 85,976,877 (GRCm39)	A67E	probably damaging	Het
Or8j3c	C	T	2: 86,253,805 (GRCm39)	G72S	possibly damaging	Het
Otud6b	T	A	4: 14,826,293 (GRCm39)	Q34L	probably damaging	Het
Parp11	C	T	6: 127,448,599 (GRCm39)	T72I	probably damaging	Het
Pbx1	T	A	1: 168,011,158 (GRCm39)	D343V	possibly damaging	Het
Phf11	T	C	14: 59,495,932 (GRCm39)		probably null	Het
Ppp1r12b	G	T	1: 134,883,471 (GRCm39)	A17E	probably benign	Het
Pramel15	C	A	4: 144,099,878 (GRCm39)	E296*	probably null	Het
Ranbp9	A	T	13: 43,588,331 (GRCm39)	I67N	probably damaging	Het
Rasgrp4	A	G	7: 28,847,832 (GRCm39)	E414G	probably damaging	Het
Rbbp5	A	G	1: 132,418,226 (GRCm39)	H15R	possibly damaging	Het
Scd2	A	G	19: 44,289,710 (GRCm39)	Y235C	probably benign	Het
Sdr16c5	C	T	4: 4,010,365 (GRCm39)	G170S	probably damaging	Het
Sh3bp4	G	T	1: 89,073,317 (GRCm39)	G722C	probably damaging	Het
Slc12a1	A	G	2: 125,008,057 (GRCm39)	I206V	probably benign	Het
Slc26a3	A	G	12: 31,503,907 (GRCm39)	D304G	probably benign	Het
Slc26a7	T	A	4: 14,532,572 (GRCm39)	D434V	possibly damaging	Het
Slc6a16	G	T	7: 44,909,390 (GRCm39)	M185I	probably benign	Het
Stat4	A	G	1: 52,121,729 (GRCm39)	I363V	possibly damaging	Het
Tgfb1i1	G	T	7: 127,847,389 (GRCm39)	M1I	probably null	Het
Thoc2l	A	G	5: 104,670,124 (GRCm39)	K1549E	possibly damaging	Het
Tmem225	T	C	9: 40,060,639 (GRCm39)	V66A	probably benign	Het
Tmtc4	T	C	14: 123,178,714 (GRCm39)		probably null	Het
Trpc4	T	A	3: 54,102,217 (GRCm39)	N38K	probably benign	Het
Ttll12	A	T	15: 83,471,314 (GRCm39)	Y218N	probably damaging	Het
Ttn	A	T	2: 76,778,769 (GRCm39)		probably null	Het
Tulp1	A	C	17: 28,570,969 (GRCm39)	Y178*	probably null	Het
Vmn2r58	A	G	7: 41,513,746 (GRCm39)	V299A	probably damaging	Het
Washc4	C	A	10: 83,419,200 (GRCm39)	Q911K	possibly damaging	Het
Wdr3	T	C	3: 100,062,252 (GRCm39)	D221G	probably benign	Het
Zan	A	T	5: 137,460,155 (GRCm39)	C1245*	probably null	Het
Zfyve9	A	C	4: 108,548,866 (GRCm39)	S773A	probably benign	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
R5183:Shmt1	UTSW	11	60,688,308 (GRCm39)	intron	probably benign
R5461:Shmt1	UTSW	11	60,685,725 (GRCm39)	missense	possibly damaging	0.94
R6014:Shmt1	UTSW	11	60,688,383 (GRCm39)	missense	probably damaging	1.00
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'- ATTCGGGAGCCTCTTGTCTC -3'
(R):5'- ATAATGGGGCGTATCTCATGG -3'

Sequencing Primer
(F):5'- TGACCTTCCTCCTGTGGACAC -3'
(R):5'- GGCGTATCTCATGGCAGAC -3'

Posted On

2016-06-06