Incidental Mutation 'R4456:Gnmt'
| ID |
329208 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Gnmt
|
| Ensembl Gene |
ENSMUSG00000002769 |
| Gene Name |
glycine N-methyltransferase |
| Synonyms |
glycine N methyl transferase |
| MMRRC Submission |
041716-MU
|
| Accession Numbers |
|
| Essential gene? |
Possibly non essential
(E-score: 0.306)
|
| Stock # |
R4456 (G1)
|
| Quality Score |
202 |
|
Status
|
Validated
|
| Chromosome |
17 |
| Chromosomal Location |
47036590-47040091 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
G to T
at 47039910 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Histidine to Glutamine
at position 56
(H56Q)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000002846
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000002840]
[ENSMUST00000002846]
|
| AlphaFold |
Q9QXF8 |
| PDB Structure |
Crystal Structure of Mouse Glycine N-Methyltransferase (Tetragonal Form) [X-RAY DIFFRACTION]
Crystal Structure of Mouse Glycine N-Methyltransferase (Monoclinic Form) [X-RAY DIFFRACTION]
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000002840
|
| SMART Domains |
Protein: ENSMUSP00000002840
Gene: ENSMUSG00000002763
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
17 |
31 |
N/A |
INTRINSIC |
|
low complexity region
|
72 |
86 |
N/A |
INTRINSIC |
|
low complexity region
|
87 |
104 |
N/A |
INTRINSIC |
|
low complexity region
|
112 |
128 |
N/A |
INTRINSIC |
|
low complexity region
|
173 |
200 |
N/A |
INTRINSIC |
|
AAA
|
463 |
598 |
6.1e-7 |
SMART |
|
AAA
|
737 |
875 |
6e-24 |
SMART |
|
Blast:AAA
|
928 |
973 |
1e-14 |
BLAST |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000002846
AA Change: H56Q
PolyPhen 2
Score 0.066 (Sensitivity: 0.94; Specificity: 0.84)
|
| SMART Domains |
Protein: ENSMUSP00000002846
Gene: ENSMUSG00000002769
AA Change: H56Q
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:Methyltransf_23
|
27 |
217 |
9e-11 |
PFAM |
|
Pfam:Methyltransf_31
|
56 |
224 |
1.3e-15 |
PFAM |
|
Pfam:Methyltransf_18
|
57 |
176 |
1.5e-15 |
PFAM |
|
Pfam:Methyltransf_25
|
61 |
169 |
1.4e-10 |
PFAM |
|
Pfam:Methyltransf_12
|
62 |
171 |
4e-12 |
PFAM |
|
Pfam:Methyltransf_11
|
62 |
173 |
2.4e-11 |
PFAM |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000144964
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000147112
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000181301
|
| Meta Mutation Damage Score |
0.0612 |
| Coding Region Coverage |
- 1x: 99.2%
- 3x: 98.6%
- 10x: 97.2%
- 20x: 95.2%
|
| Validation Efficiency |
93% (42/45) |
| MGI Phenotype |
FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The protein encoded by this gene is an enzyme that catalyzes the conversion of S-adenosyl-L-methionine (along with glycine) to S-adenosyl-L-homocysteine and sarcosine. This protein is found in the cytoplasm and acts as a homotetramer. Defects in this gene are a cause of GNMT deficiency (hypermethioninemia). Alternative splicing results in multiple transcript variants. Naturally occurring readthrough transcription occurs between the upstream CNPY3 (canopy FGF signaling regulator 3) gene and this gene and is represented with GeneID:107080644. [provided by RefSeq, Jan 2016]
PHENOTYPE: Mice homozygous for a null mutation display elevated levels of methionine and S-adenosylmethionine in the liver. Mice homozygous for another null allele exhibit hepatitis, increased hepatic glycogen storage, and hepatocellular carcinoma. [provided by MGI curators]
|
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 37 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Abca8b |
A |
G |
11: 109,833,071 (GRCm39) |
F1210L |
probably benign |
Het |
| Amfr |
C |
T |
8: 94,711,568 (GRCm39) |
A323T |
possibly damaging |
Het |
| Apob |
T |
A |
12: 8,065,445 (GRCm39) |
I4105N |
probably damaging |
Het |
| Bahd1 |
C |
T |
2: 118,746,887 (GRCm39) |
P169S |
probably damaging |
Het |
| Cdc42ep1 |
A |
G |
15: 78,734,091 (GRCm39) |
E397G |
possibly damaging |
Het |
| Cdkn2d |
C |
G |
9: 21,202,185 (GRCm39) |
V21L |
probably benign |
Het |
| Dnmt1 |
T |
C |
9: 20,821,138 (GRCm39) |
T1250A |
probably damaging |
Het |
| Dst |
A |
T |
1: 34,229,800 (GRCm39) |
K2642N |
probably benign |
Het |
| Emcn |
A |
T |
3: 137,085,608 (GRCm39) |
K69* |
probably null |
Het |
| Eya1 |
C |
T |
1: 14,253,420 (GRCm39) |
V519M |
probably damaging |
Het |
| Fbxo38 |
G |
T |
18: 62,659,320 (GRCm39) |
R326S |
probably damaging |
Het |
| Fcer1g |
A |
G |
1: 171,061,808 (GRCm39) |
S3P |
probably benign |
Het |
| Glp1r |
G |
T |
17: 31,137,949 (GRCm39) |
E127* |
probably null |
Het |
| Hectd4 |
C |
T |
5: 121,446,334 (GRCm39) |
T1513I |
possibly damaging |
Het |
| Hsd3b1 |
G |
A |
3: 98,763,459 (GRCm39) |
T48I |
probably benign |
Het |
| Kmt2c |
A |
T |
5: 25,515,210 (GRCm39) |
C2878S |
probably benign |
Het |
| Loxhd1 |
A |
G |
18: 77,486,785 (GRCm39) |
Y1290C |
probably damaging |
Het |
| Mkln1 |
A |
G |
6: 31,403,707 (GRCm39) |
Y76C |
probably damaging |
Het |
| Mri1 |
C |
A |
8: 84,983,035 (GRCm39) |
A129S |
probably benign |
Het |
| Mroh2b |
A |
T |
15: 4,977,407 (GRCm39) |
H1253L |
probably benign |
Het |
| Mslnl |
G |
A |
17: 25,961,908 (GRCm39) |
V128M |
probably damaging |
Het |
| Mthfsd |
C |
T |
8: 121,832,504 (GRCm39) |
V63I |
possibly damaging |
Het |
| Naip2 |
T |
A |
13: 100,291,419 (GRCm39) |
H1173L |
probably benign |
Het |
| Nbea |
A |
G |
3: 55,551,205 (GRCm39) |
V2653A |
probably benign |
Het |
| Nckap5 |
A |
T |
1: 125,842,472 (GRCm39) |
|
probably benign |
Het |
| Notch4 |
G |
A |
17: 34,802,807 (GRCm39) |
V1378M |
probably damaging |
Het |
| Or51a42 |
A |
G |
7: 103,708,507 (GRCm39) |
S101P |
possibly damaging |
Het |
| Rab36 |
G |
A |
10: 74,880,328 (GRCm39) |
V63I |
probably damaging |
Het |
| Rasl12 |
A |
G |
9: 65,305,866 (GRCm39) |
K7R |
probably null |
Het |
| Rnf4 |
A |
G |
5: 34,508,705 (GRCm39) |
Y189C |
probably benign |
Het |
| Shroom3 |
A |
G |
5: 93,088,858 (GRCm39) |
H536R |
probably benign |
Het |
| Slc2a4 |
G |
A |
11: 69,834,148 (GRCm39) |
|
probably benign |
Het |
| Tbc1d5 |
A |
C |
17: 51,089,369 (GRCm39) |
S604A |
probably damaging |
Het |
| Tcp11l1 |
A |
T |
2: 104,514,567 (GRCm39) |
V400E |
probably damaging |
Het |
| Tom1l2 |
G |
T |
11: 60,243,641 (GRCm39) |
|
probably benign |
Het |
| Ttc28 |
AC |
A |
5: 111,371,924 (GRCm39) |
|
probably null |
Het |
| Txndc15 |
A |
G |
13: 55,865,977 (GRCm39) |
D147G |
possibly damaging |
Het |
|
| Other mutations in Gnmt |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL01351:Gnmt
|
APN |
17 |
47,037,606 (GRCm39) |
missense |
probably benign |
0.28 |
|
health_nut
|
UTSW |
17 |
47,037,271 (GRCm39) |
missense |
probably damaging |
1.00 |
|
impulsive
|
UTSW |
17 |
47,036,892 (GRCm39) |
missense |
probably damaging |
1.00 |
|
Incautious
|
UTSW |
17 |
47,038,313 (GRCm39) |
missense |
probably damaging |
1.00 |
|
rash
|
UTSW |
17 |
47,036,662 (GRCm39) |
utr 3 prime |
probably benign |
|
|
R0480:Gnmt
|
UTSW |
17 |
47,036,854 (GRCm39) |
missense |
probably benign |
0.06 |
|
R0938:Gnmt
|
UTSW |
17 |
47,037,271 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R0939:Gnmt
|
UTSW |
17 |
47,037,271 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R0940:Gnmt
|
UTSW |
17 |
47,037,271 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R0941:Gnmt
|
UTSW |
17 |
47,037,271 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R3619:Gnmt
|
UTSW |
17 |
47,039,963 (GRCm39) |
missense |
possibly damaging |
0.63 |
|
R4173:Gnmt
|
UTSW |
17 |
47,037,047 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4498:Gnmt
|
UTSW |
17 |
47,036,662 (GRCm39) |
utr 3 prime |
probably benign |
|
|
R4659:Gnmt
|
UTSW |
17 |
47,036,892 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4669:Gnmt
|
UTSW |
17 |
47,037,225 (GRCm39) |
nonsense |
probably null |
|
|
R4827:Gnmt
|
UTSW |
17 |
47,038,245 (GRCm39) |
missense |
possibly damaging |
0.77 |
|
R5112:Gnmt
|
UTSW |
17 |
47,037,256 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5133:Gnmt
|
UTSW |
17 |
47,036,860 (GRCm39) |
missense |
probably benign |
|
|
R5797:Gnmt
|
UTSW |
17 |
47,037,305 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7423:Gnmt
|
UTSW |
17 |
47,037,066 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7825:Gnmt
|
UTSW |
17 |
47,040,019 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R8785:Gnmt
|
UTSW |
17 |
47,038,313 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8861:Gnmt
|
UTSW |
17 |
47,037,618 (GRCm39) |
missense |
probably damaging |
1.00 |
|
| Predicted Primers |
PCR Primer
(F):5'- CACTGTTTCGGCAGATGCTC -3'
(R):5'- TTGCCAGAGGATTATAAGTGCGG -3'
Sequencing Primer
(F):5'- TCGGCAGATGCTCTCCCATG -3'
(R):5'- ATCGCGTGGCCTGAGAG -3'
|
| Posted On |
2015-07-21 |
Incidental Mutation