Mutagenetix > Incidental Mutations

Incidental Mutation 'IGL02088:Shmt1'

279322

Institutional Source

Australian Phenomics Network (link to record)

Gene Symbol

Shmt1

Ensembl Gene

ENSMUSG00000020534

Gene Name

serine hydroxymethyltransferase 1 (soluble)

Synonyms

mshmt1, Shmt, mshmt2, mshmt

Accession Numbers

Is this an essential gene?

Non essential (E-score: 0.000) question?

Stock #

IGL02088

Quality Score

Status

Chromosome

Chromosomal Location

60788104-60811718 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 60789653 bp

Zygosity

Heterozygous

Amino Acid Change

Threonine to Alanine at position 403 (T403A)

Ref Sequence

ENSEMBL: ENSMUSP00000018744 (fasta)

Gene Model

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

PDB Structure

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

Predicted Effect

probably damaging
Transcript: ENSMUST00000018744
AA Change: T403A

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

SMART Domains

Protein: ENSMUSP00000018744
Gene: ENSMUSG00000020534
AA Change: T403A

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: 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

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

unknown
Transcript: ENSMUST00000174719
AA Change: T363A

SMART Domains

Protein: ENSMUSP00000134318
Gene: ENSMUSG00000020534
AA Change: T363A

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

Validation Efficiency

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: 38 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Ackr4	T	C	9: 104,098,881	E289G	probably damaging	Het
Aldh1l1	A	T	6: 90,580,590		probably benign	Het
Ampd3	T	A	7: 110,793,686	D220E	probably benign	Het
Ank3	T	C	10: 69,999,373	V136A	probably damaging	Het
Atg14	T	C	14: 47,542,859	K486R	probably benign	Het
Axin1	A	G	17: 26,188,695	I637V	probably benign	Het
Axin2	T	A	11: 108,923,616	F110Y	probably damaging	Het
Cdh12	A	T	15: 21,480,339	K214*	probably null	Het
Cfap44	A	C	16: 44,451,628	E1248A	possibly damaging	Het
Cryba4	A	G	5: 112,251,009		probably benign	Het
Cyp2c68	A	G	19: 39,703,521		probably benign	Het
Dnah5	G	T	15: 28,459,118		probably null	Het
Dok3	A	T	13: 55,524,370	V165E	probably damaging	Het
Etl4	A	T	2: 20,806,548	R1147S	probably damaging	Het
Fam212a	A	G	9: 107,984,457	F220S	probably damaging	Het
Fbxl6	G	T	15: 76,535,906	C502*	probably null	Het
Gp2	A	T	7: 119,454,469	Y90N	probably damaging	Het
H1fnt	G	T	15: 98,257,178	T30K	probably damaging	Het
Itfg2	A	G	6: 128,411,606	V306A	probably benign	Het
Lrig2	T	C	3: 104,467,108	Y219C	probably damaging	Het
Mccc1	A	T	3: 35,974,202	I485N	probably damaging	Het
Mettl25	A	G	10: 105,823,250	F391L	probably damaging	Het
Muc19	C	T	15: 91,891,168		noncoding transcript	Het
Muc2	T	C	7: 141,751,504	C182R	probably damaging	Het
Nlrp4g	T	C	9: 124,350,453		noncoding transcript	Het
Nms	A	G	1: 38,939,277		probably benign	Het
Nr3c1	T	C	18: 39,424,391	N503S	probably damaging	Het
Olfr1495	T	C	19: 13,768,666	F108S	probably damaging	Het
Olfr186	A	G	16: 59,027,052	L285P	probably damaging	Het
Olfr828	C	T	9: 18,815,923	V124I	probably benign	Het
Pcdhb5	G	A	18: 37,321,959	S464N	probably benign	Het
Pcgf6	T	C	19: 47,050,804	T6A	unknown	Het
Rdx	A	G	9: 52,060,883		probably benign	Het
Slc35d1	A	G	4: 103,211,325	F148L	probably benign	Het
Tk1	A	G	11: 117,824,665		probably benign	Het
Tnks	T	A	8: 34,839,994	I1134F	possibly damaging	Het
Ttn	A	G	2: 76,726,691	V29990A	probably damaging	Het
Zcchc11	A	G	4: 108,512,218		probably benign	Het

Other mutations in Shmt1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
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
R7215:Shmt1	UTSW	11	60801535	missense	probably damaging	0.99
R7514:Shmt1	UTSW	11	60801986	missense	probably damaging	1.00

Posted On

2015-04-16