Incidental Mutation 'R7390:Gldc'
| ID |
573401 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Gldc
|
| Ensembl Gene |
ENSMUSG00000024827 |
| Gene Name |
glycine decarboxylase |
| Synonyms |
b2b2679Clo, D030049L12Rik, D19Wsu57e |
| MMRRC Submission |
045472-MU
|
| Accession Numbers |
|
| Essential gene? |
Essential
(E-score: 1.000)
|
| Stock # |
R7390 (G1)
|
| Quality Score |
225.009 |
|
Status
|
Validated
|
| Chromosome |
19 |
| Chromosomal Location |
30075847-30152829 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to T
at 30077314 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Serine to Threonine
at position 953
(S953T)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000025778
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000025778]
|
| AlphaFold |
Q91W43 |
| Predicted Effect |
possibly damaging
Transcript: ENSMUST00000025778
AA Change: S953T
PolyPhen 2
Score 0.462 (Sensitivity: 0.89; Specificity: 0.90)
|
| SMART Domains |
Protein: ENSMUSP00000025778
Gene: ENSMUSG00000024827
AA Change: S953T
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
5 |
28 |
N/A |
INTRINSIC |
|
low complexity region
|
33 |
56 |
N/A |
INTRINSIC |
|
Pfam:GDC-P
|
70 |
493 |
1.1e-202 |
PFAM |
|
low complexity region
|
504 |
515 |
N/A |
INTRINSIC |
|
Pfam:GDC-P
|
519 |
798 |
6.5e-8 |
PFAM |
|
Pfam:Beta_elim_lyase
|
589 |
745 |
2e-10 |
PFAM |
|
| Coding Region Coverage |
- 1x: 100.0%
- 3x: 99.9%
- 10x: 99.7%
- 20x: 99.0%
|
| Validation Efficiency |
97% (66/68) |
| MGI Phenotype |
FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] Degradation of glycine is brought about by the glycine cleavage system, which is composed of four mitochondrial protein components: P protein (a pyridoxal phosphate-dependent glycine decarboxylase), H protein (a lipoic acid-containing protein), T protein (a tetrahydrofolate-requiring enzyme), and L protein (a lipoamide dehydrogenase). The protein encoded by this gene is the P protein, which binds to glycine and enables the methylamine group from glycine to be transferred to the T protein. Defects in this gene are a cause of nonketotic hyperglycinemia (NKH).[provided by RefSeq, Jan 2010]
PHENOTYPE: Hypomorphic mutants show a developmental delay, hyperglycinemia, altered folate profiles, neural tube defects and postnatal lethality, while survivors show hydrocephaly and premature death. Homozygotes for an ENU allele show omphalocele and severe cardiovascular, craniofacial, renal and eye defects. [provided by MGI curators]
|
| Allele List at MGI |
All alleles(6) : Targeted, other(2) Gene trapped(4)
|
| Other mutations in this stock |
Total: 68 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 4930486L24Rik |
A |
T |
13: 60,992,152 (GRCm39) |
D291E |
probably benign |
Het |
| Abca9 |
C |
T |
11: 110,036,487 (GRCm39) |
V541I |
probably benign |
Het |
| Adamts15 |
A |
T |
9: 30,822,404 (GRCm39) |
|
probably null |
Het |
| Adgrg7 |
A |
G |
16: 56,553,207 (GRCm39) |
I630T |
probably damaging |
Het |
| Ahnak |
A |
G |
19: 8,980,569 (GRCm39) |
I618V |
probably benign |
Het |
| Amotl2 |
T |
A |
9: 102,608,889 (GRCm39) |
V801E |
probably damaging |
Het |
| Ankrd17 |
T |
C |
5: 90,430,779 (GRCm39) |
T1002A |
probably benign |
Het |
| Bmp7 |
C |
T |
2: 172,711,998 (GRCm39) |
D409N |
probably damaging |
Het |
| Bpifb2 |
A |
G |
2: 153,731,726 (GRCm39) |
N293S |
possibly damaging |
Het |
| Ccdc162 |
A |
G |
10: 41,510,044 (GRCm39) |
C854R |
probably benign |
Het |
| Ccdc171 |
A |
G |
4: 83,736,304 (GRCm39) |
E1225G |
probably damaging |
Het |
| Cep350 |
T |
C |
1: 155,741,833 (GRCm39) |
E2146G |
possibly damaging |
Het |
| Ces1a |
A |
C |
8: 93,771,469 (GRCm39) |
|
probably null |
Het |
| Cfap45 |
T |
G |
1: 172,368,925 (GRCm39) |
D444E |
probably benign |
Het |
| Cfap61 |
T |
C |
2: 145,843,802 (GRCm39) |
V296A |
probably benign |
Het |
| Cgnl1 |
C |
T |
9: 71,552,931 (GRCm39) |
R1011H |
probably benign |
Het |
| Cops4 |
C |
T |
5: 100,691,741 (GRCm39) |
R347C |
probably damaging |
Het |
| D16Ertd472e |
G |
T |
16: 78,344,576 (GRCm39) |
D177E |
probably benign |
Het |
| Dcdc2a |
T |
C |
13: 25,291,600 (GRCm39) |
V195A |
possibly damaging |
Het |
| Dipk2a |
A |
G |
9: 94,419,436 (GRCm39) |
S165P |
probably damaging |
Het |
| Dpagt1 |
G |
A |
9: 44,243,319 (GRCm39) |
V285I |
probably benign |
Het |
| Dspp |
G |
T |
5: 104,323,552 (GRCm39) |
A232S |
probably damaging |
Het |
| Efcab3 |
T |
C |
11: 104,615,411 (GRCm39) |
I726T |
possibly damaging |
Het |
| Ephx2 |
G |
A |
14: 66,347,904 (GRCm39) |
|
|
Het |
| Fat1 |
T |
C |
8: 45,405,511 (GRCm39) |
V754A |
possibly damaging |
Het |
| Fstl3 |
G |
A |
10: 79,615,865 (GRCm39) |
C117Y |
probably damaging |
Het |
| Gm1123 |
T |
C |
9: 98,893,033 (GRCm39) |
N315S |
probably benign |
Het |
| Golga2 |
A |
G |
2: 32,178,202 (GRCm39) |
E37G |
|
Het |
| Gpr139 |
T |
A |
7: 118,743,835 (GRCm39) |
Q250L |
probably benign |
Het |
| Grik3 |
C |
T |
4: 125,543,532 (GRCm39) |
R283C |
probably damaging |
Het |
| Haao |
A |
C |
17: 84,154,081 (GRCm39) |
V22G |
probably damaging |
Het |
| Hspg2 |
T |
A |
4: 137,266,490 (GRCm39) |
F1884I |
probably damaging |
Het |
| Hyal3 |
G |
A |
9: 107,462,166 (GRCm39) |
G67S |
probably damaging |
Het |
| Kbtbd3 |
T |
A |
9: 4,330,424 (GRCm39) |
I266K |
probably benign |
Het |
| Klhl26 |
A |
C |
8: 70,905,499 (GRCm39) |
L137R |
probably damaging |
Het |
| Krt15 |
A |
T |
11: 100,026,386 (GRCm39) |
V100E |
possibly damaging |
Het |
| Lars1 |
A |
G |
18: 42,343,083 (GRCm39) |
|
probably null |
Het |
| Lats1 |
C |
T |
10: 7,577,859 (GRCm39) |
Q328* |
probably null |
Het |
| Lingo3 |
G |
A |
10: 80,670,463 (GRCm39) |
T489I |
probably damaging |
Het |
| Lmtk2 |
T |
C |
5: 144,066,261 (GRCm39) |
V65A |
possibly damaging |
Het |
| Lysmd1 |
T |
C |
3: 95,045,795 (GRCm39) |
S211P |
probably damaging |
Het |
| Med15 |
C |
T |
16: 17,540,626 (GRCm39) |
S21N |
unknown |
Het |
| Nav1 |
T |
C |
1: 135,512,656 (GRCm39) |
T135A |
probably benign |
Het |
| Nt5c1a |
G |
C |
4: 123,102,272 (GRCm39) |
R66T |
probably benign |
Het |
| Pclo |
T |
C |
5: 14,732,024 (GRCm39) |
Y3509H |
unknown |
Het |
| Pkp4 |
G |
A |
2: 59,140,484 (GRCm39) |
G397R |
possibly damaging |
Het |
| Ppp1r21 |
G |
A |
17: 88,856,958 (GRCm39) |
A138T |
probably benign |
Het |
| Pum3 |
A |
T |
19: 27,401,642 (GRCm39) |
V136D |
probably benign |
Het |
| Rab11fip3 |
A |
T |
17: 26,287,126 (GRCm39) |
D342E |
possibly damaging |
Het |
| Rcvrn |
T |
A |
11: 67,590,883 (GRCm39) |
W156R |
probably damaging |
Het |
| Rspry1 |
C |
T |
8: 95,349,813 (GRCm39) |
T67I |
probably benign |
Het |
| Serpina1d |
T |
C |
12: 103,734,037 (GRCm39) |
D89G |
possibly damaging |
Het |
| Sgsm3 |
T |
A |
15: 80,893,021 (GRCm39) |
V366E |
possibly damaging |
Het |
| Shank3 |
T |
G |
15: 89,433,515 (GRCm39) |
L1420R |
probably benign |
Het |
| Sirpb1b |
A |
T |
3: 15,608,100 (GRCm39) |
L215* |
probably null |
Het |
| Slc16a13 |
C |
T |
11: 70,109,797 (GRCm39) |
V235I |
probably benign |
Het |
| Slc16a14 |
T |
C |
1: 84,907,187 (GRCm39) |
D29G |
probably benign |
Het |
| Speer1a |
T |
C |
5: 11,394,879 (GRCm39) |
V122A |
probably benign |
Het |
| Spns2 |
T |
A |
11: 72,347,704 (GRCm39) |
T329S |
possibly damaging |
Het |
| Sufu |
G |
A |
19: 46,439,108 (GRCm39) |
|
probably null |
Het |
| Tll2 |
A |
G |
19: 41,108,608 (GRCm39) |
|
probably null |
Het |
| Trim10 |
G |
A |
17: 37,180,773 (GRCm39) |
M1I |
probably null |
Het |
| Trim42 |
A |
C |
9: 97,241,182 (GRCm39) |
N683K |
probably damaging |
Het |
| Trmt5 |
A |
G |
12: 73,328,394 (GRCm39) |
S270P |
probably damaging |
Het |
| Vmn1r59 |
C |
A |
7: 5,456,986 (GRCm39) |
R258L |
possibly damaging |
Het |
| Vmn2r32 |
A |
G |
7: 7,482,851 (GRCm39) |
L41S |
probably benign |
Het |
| Vmn2r93 |
A |
T |
17: 18,525,329 (GRCm39) |
E329V |
probably damaging |
Het |
| Ywhae |
G |
T |
11: 75,655,487 (GRCm39) |
E253* |
probably null |
Het |
|
| Other mutations in Gldc |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL00160:Gldc
|
APN |
19 |
30,092,640 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL01016:Gldc
|
APN |
19 |
30,110,893 (GRCm39) |
missense |
possibly damaging |
0.93 |
|
IGL01112:Gldc
|
APN |
19 |
30,135,913 (GRCm39) |
critical splice donor site |
probably null |
|
|
IGL01510:Gldc
|
APN |
19 |
30,091,121 (GRCm39) |
critical splice donor site |
probably null |
|
|
IGL01516:Gldc
|
APN |
19 |
30,076,432 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL01598:Gldc
|
APN |
19 |
30,111,156 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL01646:Gldc
|
APN |
19 |
30,078,165 (GRCm39) |
missense |
possibly damaging |
0.61 |
|
IGL02024:Gldc
|
APN |
19 |
30,078,227 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL02125:Gldc
|
APN |
19 |
30,124,641 (GRCm39) |
missense |
probably benign |
0.03 |
|
IGL02548:Gldc
|
APN |
19 |
30,077,299 (GRCm39) |
missense |
probably benign |
|
|
IGL02711:Gldc
|
APN |
19 |
30,122,546 (GRCm39) |
critical splice donor site |
probably null |
|
|
IGL02818:Gldc
|
APN |
19 |
30,113,909 (GRCm39) |
missense |
probably damaging |
0.99 |
|
IGL02982:Gldc
|
APN |
19 |
30,122,545 (GRCm39) |
critical splice donor site |
probably null |
|
|
IGL03165:Gldc
|
APN |
19 |
30,076,393 (GRCm39) |
missense |
possibly damaging |
0.61 |
|
jojoba
|
UTSW |
19 |
30,110,912 (GRCm39) |
missense |
probably damaging |
1.00 |
|
miserable
|
UTSW |
19 |
30,128,936 (GRCm39) |
missense |
probably damaging |
1.00 |
|
Urchin
|
UTSW |
19 |
30,096,002 (GRCm39) |
missense |
probably damaging |
0.98 |
|
I2289:Gldc
|
UTSW |
19 |
30,124,576 (GRCm39) |
nonsense |
probably null |
|
|
R0180:Gldc
|
UTSW |
19 |
30,078,217 (GRCm39) |
missense |
possibly damaging |
0.95 |
|
R0269:Gldc
|
UTSW |
19 |
30,096,002 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R0277:Gldc
|
UTSW |
19 |
30,093,851 (GRCm39) |
missense |
possibly damaging |
0.84 |
|
R1085:Gldc
|
UTSW |
19 |
30,128,828 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1159:Gldc
|
UTSW |
19 |
30,138,162 (GRCm39) |
intron |
probably benign |
|
|
R1500:Gldc
|
UTSW |
19 |
30,091,225 (GRCm39) |
missense |
possibly damaging |
0.88 |
|
R1507:Gldc
|
UTSW |
19 |
30,096,038 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1592:Gldc
|
UTSW |
19 |
30,138,077 (GRCm39) |
intron |
probably benign |
|
|
R1593:Gldc
|
UTSW |
19 |
30,091,150 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1675:Gldc
|
UTSW |
19 |
30,120,853 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1869:Gldc
|
UTSW |
19 |
30,116,732 (GRCm39) |
missense |
probably benign |
|
|
R1965:Gldc
|
UTSW |
19 |
30,114,513 (GRCm39) |
nonsense |
probably null |
|
|
R2312:Gldc
|
UTSW |
19 |
30,078,226 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R2425:Gldc
|
UTSW |
19 |
30,109,190 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R3836:Gldc
|
UTSW |
19 |
30,096,075 (GRCm39) |
splice site |
probably benign |
|
|
R3837:Gldc
|
UTSW |
19 |
30,096,075 (GRCm39) |
splice site |
probably benign |
|
|
R3839:Gldc
|
UTSW |
19 |
30,096,075 (GRCm39) |
splice site |
probably benign |
|
|
R4191:Gldc
|
UTSW |
19 |
30,123,058 (GRCm39) |
missense |
probably damaging |
0.96 |
|
R4380:Gldc
|
UTSW |
19 |
30,138,168 (GRCm39) |
intron |
probably benign |
|
|
R4508:Gldc
|
UTSW |
19 |
30,120,807 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4570:Gldc
|
UTSW |
19 |
30,151,839 (GRCm39) |
missense |
probably benign |
|
|
R4655:Gldc
|
UTSW |
19 |
30,138,102 (GRCm39) |
intron |
probably benign |
|
|
R4842:Gldc
|
UTSW |
19 |
30,111,132 (GRCm39) |
missense |
possibly damaging |
0.94 |
|
R5070:Gldc
|
UTSW |
19 |
30,095,998 (GRCm39) |
missense |
possibly damaging |
0.84 |
|
R5085:Gldc
|
UTSW |
19 |
30,128,936 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5268:Gldc
|
UTSW |
19 |
30,123,125 (GRCm39) |
missense |
probably damaging |
0.96 |
|
R5368:Gldc
|
UTSW |
19 |
30,135,921 (GRCm39) |
missense |
probably benign |
|
|
R5718:Gldc
|
UTSW |
19 |
30,088,172 (GRCm39) |
nonsense |
probably null |
|
|
R5878:Gldc
|
UTSW |
19 |
30,120,867 (GRCm39) |
splice site |
probably null |
|
|
R6192:Gldc
|
UTSW |
19 |
30,111,172 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R6453:Gldc
|
UTSW |
19 |
30,093,917 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R6777:Gldc
|
UTSW |
19 |
30,110,912 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R6865:Gldc
|
UTSW |
19 |
30,111,162 (GRCm39) |
missense |
possibly damaging |
0.92 |
|
R7332:Gldc
|
UTSW |
19 |
30,093,926 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R7647:Gldc
|
UTSW |
19 |
30,096,067 (GRCm39) |
missense |
probably damaging |
0.96 |
|
R8081:Gldc
|
UTSW |
19 |
30,135,987 (GRCm39) |
frame shift |
probably null |
|
|
R8171:Gldc
|
UTSW |
19 |
30,111,161 (GRCm39) |
missense |
probably benign |
0.24 |
|
R8321:Gldc
|
UTSW |
19 |
30,120,807 (GRCm39) |
nonsense |
probably null |
|
|
R8374:Gldc
|
UTSW |
19 |
30,114,594 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8503:Gldc
|
UTSW |
19 |
30,077,254 (GRCm39) |
missense |
probably benign |
0.26 |
|
R8510:Gldc
|
UTSW |
19 |
30,093,905 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8785:Gldc
|
UTSW |
19 |
30,092,634 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8818:Gldc
|
UTSW |
19 |
30,078,212 (GRCm39) |
missense |
probably benign |
0.05 |
|
R8820:Gldc
|
UTSW |
19 |
30,078,212 (GRCm39) |
missense |
probably benign |
0.05 |
|
R8829:Gldc
|
UTSW |
19 |
30,078,212 (GRCm39) |
missense |
probably benign |
0.05 |
|
R8830:Gldc
|
UTSW |
19 |
30,078,212 (GRCm39) |
missense |
probably benign |
0.05 |
|
R8859:Gldc
|
UTSW |
19 |
30,116,779 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8887:Gldc
|
UTSW |
19 |
30,111,156 (GRCm39) |
missense |
possibly damaging |
0.94 |
|
R8935:Gldc
|
UTSW |
19 |
30,109,093 (GRCm39) |
missense |
probably benign |
0.00 |
|
R8940:Gldc
|
UTSW |
19 |
30,128,884 (GRCm39) |
missense |
probably benign |
|
|
R9070:Gldc
|
UTSW |
19 |
30,080,404 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9100:Gldc
|
UTSW |
19 |
30,077,314 (GRCm39) |
missense |
possibly damaging |
0.81 |
|
R9144:Gldc
|
UTSW |
19 |
30,114,593 (GRCm39) |
missense |
|
|
|
R9163:Gldc
|
UTSW |
19 |
30,111,686 (GRCm39) |
missense |
probably benign |
0.13 |
|
R9429:Gldc
|
UTSW |
19 |
30,091,172 (GRCm39) |
missense |
possibly damaging |
0.88 |
|
Z1177:Gldc
|
UTSW |
19 |
30,123,148 (GRCm39) |
missense |
possibly damaging |
0.61 |
|
Z1177:Gldc
|
UTSW |
19 |
30,088,179 (GRCm39) |
missense |
probably damaging |
0.99 |
|
Z1177:Gldc
|
UTSW |
19 |
30,088,178 (GRCm39) |
missense |
probably damaging |
1.00 |
|
| Predicted Primers |
PCR Primer
(F):5'- TTCACGGGCTATCCTAGATACAC -3'
(R):5'- AGGGAGACTCTTCCTCATGG -3'
Sequencing Primer
(F):5'- CTTTATATAATGAGACTGTGGATGGG -3'
(R):5'- CATGGTATGAGCTATGTTGTCAG -3'
|
| Posted On |
2019-09-13 |
Incidental Mutation