Mutagenetix > Incidental Mutation

Incidental Mutation 'R5070:Gldc'

388724

Institutional Source

Beutler Lab

Gene Symbol

Gldc

Ensembl Gene

ENSMUSG00000024827

Gene Name

glycine decarboxylase

Synonyms

b2b2679Clo, D030049L12Rik, D19Wsu57e

MMRRC Submission

042660-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R5070 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

30075847-30152829 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 30095998 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Glutamine to Arginine at position 671 (Q671R)

Ref Sequence

ENSEMBL: ENSMUSP00000025778 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000025778]

AlphaFold

Q91W43

Predicted Effect

possibly damaging
Transcript: ENSMUST00000025778
AA Change: Q671R

PolyPhen 2 Score 0.842 (Sensitivity: 0.83; Specificity: 0.93)

SMART Domains

Protein: ENSMUSP00000025778
Gene: ENSMUSG00000024827
AA Change: Q671R

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: 99.2%
3x: 98.5%
10x: 96.6%
20x: 93.0%

Validation Efficiency

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: 114 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
3425401B19Rik	A	G	14: 32,383,749 (GRCm39)	S739P	possibly damaging	Het
Acacb	T	C	5: 114,384,089 (GRCm39)	I2206T	possibly damaging	Het
Actn2	A	G	13: 12,303,408 (GRCm39)	I464T	possibly damaging	Het
AI987944	C	T	7: 41,024,748 (GRCm39)	G77D	probably benign	Het
Ankar	T	C	1: 72,719,369 (GRCm39)		probably null	Het
Armc9	A	T	1: 86,184,959 (GRCm39)	H670L	probably benign	Het
Arvcf	A	G	16: 18,217,736 (GRCm39)	Y412C	probably damaging	Het
Baiap3	A	T	17: 25,468,082 (GRCm39)	C283S	probably damaging	Het
Bend3	A	T	10: 43,369,681 (GRCm39)	E11D	probably damaging	Het
Birc6	C	T	17: 74,872,967 (GRCm39)	R409C	probably damaging	Het
Cds2	T	A	2: 132,144,008 (GRCm39)	Y4*	probably null	Het
Celsr1	G	T	15: 85,823,335 (GRCm39)	P1691Q	possibly damaging	Het
Chmp1a	A	T	8: 123,933,054 (GRCm39)	V133E	probably benign	Het
Cnbd2	T	C	2: 156,177,318 (GRCm39)	V92A	probably damaging	Het
Comp	G	A	8: 70,829,145 (GRCm39)	G272S	probably benign	Het
Csnk1a1	T	A	18: 61,688,852 (GRCm39)	F11I	probably benign	Het
Ctse	A	G	1: 131,595,917 (GRCm39)	D203G	probably damaging	Het
Cyp1b1	T	A	17: 80,018,040 (GRCm39)	M372L	probably benign	Het
Cyp2c66	T	A	19: 39,151,914 (GRCm39)	S210T	probably benign	Het
Dnah1	G	A	14: 31,004,375 (GRCm39)	P2385S	probably benign	Het
Dsp	A	C	13: 38,381,099 (GRCm39)	T2615P	possibly damaging	Het
Eif4g3	A	G	4: 137,873,610 (GRCm39)	T682A	probably benign	Het
Enpp2	T	C	15: 54,727,450 (GRCm39)	Y513C	probably damaging	Het
Ercc6	T	C	14: 32,292,020 (GRCm39)	V1128A	probably benign	Het
Fam136b-ps	C	T	15: 31,276,862 (GRCm39)		probably benign	Het
Fbxl7	T	A	15: 26,789,640 (GRCm39)	H29L	probably benign	Het
Fbxw22	A	G	9: 109,214,183 (GRCm39)	V211A	probably benign	Het
Frk	A	T	10: 34,360,280 (GRCm39)	K94*	probably null	Het
G0s2	T	A	1: 192,954,870 (GRCm39)	E71D	probably damaging	Het
Gfpt1	A	G	6: 87,030,727 (GRCm39)		probably null	Het
Gga1	A	G	15: 78,776,217 (GRCm39)	D420G	possibly damaging	Het
Gpc6	A	G	14: 117,424,181 (GRCm39)	T90A	probably benign	Het
Gucy2g	C	A	19: 55,218,219 (GRCm39)	V410F	probably damaging	Het
Ifnlr1	T	C	4: 135,431,509 (GRCm39)	S233P	probably benign	Het
Ighv1-9	A	T	12: 114,547,377 (GRCm39)	W55R	probably damaging	Het
Igsf10	T	A	3: 59,235,714 (GRCm39)	H1489L	probably benign	Het
Il17re	T	C	6: 113,435,971 (GRCm39)	L39P	probably damaging	Het
Irag1	A	G	7: 110,524,519 (GRCm39)	S208P	probably benign	Het
Kcna2	T	A	3: 107,011,953 (GRCm39)	V178D	probably damaging	Het
Kcnk3	A	G	5: 30,779,730 (GRCm39)	H260R	possibly damaging	Het
Kctd19	T	C	8: 106,118,631 (GRCm39)	Y287C	probably damaging	Het
Klhl28	A	T	12: 65,004,486 (GRCm39)	M9K	probably benign	Het
Lama2	A	G	10: 27,226,247 (GRCm39)		probably null	Het
Lrrc27	A	T	7: 138,794,715 (GRCm39)	D26V	probably damaging	Het
Mcm4	A	G	16: 15,443,434 (GRCm39)	S830P	probably damaging	Het
Mei1	T	A	15: 81,961,804 (GRCm39)	C188S	possibly damaging	Het
Mettl13	C	T	1: 162,373,468 (GRCm39)	R261H	possibly damaging	Het
Mex3a	A	T	3: 88,443,694 (GRCm39)	I257F	probably damaging	Het
Mib1	A	G	18: 10,793,002 (GRCm39)	E646G	probably damaging	Het
Mier2	T	C	10: 79,385,411 (GRCm39)	D139G	probably benign	Het
Mmp14	T	A	14: 54,676,570 (GRCm39)	Y372N	probably damaging	Het
Myh14	A	G	7: 44,265,672 (GRCm39)	V1569A	possibly damaging	Het
Myo18b	T	C	5: 112,909,212 (GRCm39)	E1977G	probably damaging	Het
Myo3b	T	C	2: 70,083,456 (GRCm39)	L675P	probably damaging	Het
N4bp1	A	G	8: 87,587,165 (GRCm39)	V591A	probably damaging	Het
Nedd9	C	A	13: 41,470,074 (GRCm39)	V360L	probably benign	Het
Oit3	C	T	10: 59,259,849 (GRCm39)	R518H	probably damaging	Het
Or10ag57	T	G	2: 87,218,507 (GRCm39)	C153G	probably damaging	Het
Or11g2	A	G	14: 50,855,931 (GRCm39)	N84S	probably benign	Het
Or11g2	T	A	14: 50,856,197 (GRCm39)	C173S	probably damaging	Het
Or11h4	C	A	14: 50,974,531 (GRCm39)	L29F	probably benign	Het
Or1j14	T	A	2: 36,417,778 (GRCm39)	M118K	probably damaging	Het
Or2aj6	A	G	16: 19,443,742 (GRCm39)	I36T	possibly damaging	Het
Or2j6	A	G	7: 139,980,482 (GRCm39)	V159A	probably benign	Het
Or9s23	T	A	1: 92,501,135 (GRCm39)	S81T	probably damaging	Het
Otx1	C	A	11: 21,947,037 (GRCm39)	A91S	probably damaging	Het
Pask	A	T	1: 93,258,596 (GRCm39)	C251S	probably damaging	Het
Pdzk1	A	T	3: 96,757,637 (GRCm39)	D31V	probably benign	Het
Pmfbp1	A	T	8: 110,256,787 (GRCm39)	Q497L	probably damaging	Het
Pofut1	T	C	2: 153,103,486 (GRCm39)		probably benign	Het
Polr2h	A	G	16: 20,540,716 (GRCm39)	N95S	probably damaging	Het
Pou2f3	A	G	9: 43,056,578 (GRCm39)	V93A	possibly damaging	Het
Ppfia1	G	A	7: 144,068,210 (GRCm39)	Q446*	probably null	Het
Prkd1	A	T	12: 50,441,405 (GRCm39)	L327*	probably null	Het
Prrt4	T	C	6: 29,177,511 (GRCm39)	E86G	probably benign	Het
Psen2	T	C	1: 180,056,422 (GRCm39)	I393V	probably benign	Het
Psma2	G	A	13: 14,790,613 (GRCm39)	V20I	probably benign	Het
Qser1	C	T	2: 104,617,627 (GRCm39)	V1062I	possibly damaging	Het
Rab11b	G	T	17: 33,967,855 (GRCm39)	A114D	probably damaging	Het
Rag1	A	T	2: 101,472,656 (GRCm39)	W829R	probably damaging	Het
Rgl3	A	G	9: 21,899,340 (GRCm39)		probably null	Het
Rgs8	C	T	1: 153,541,650 (GRCm39)	T3I	probably damaging	Het
Rnf17	T	C	14: 56,743,385 (GRCm39)	V1317A	probably damaging	Het
Rps6kb2	A	T	19: 4,213,227 (GRCm39)	D6E	probably damaging	Het
Shisal1	G	T	15: 84,304,364 (GRCm39)	A14E	possibly damaging	Het
Skint5	T	A	4: 113,652,735 (GRCm39)	I630F	unknown	Het
Skint7	T	C	4: 111,841,331 (GRCm39)	L257P	probably damaging	Het
Slc11a1	G	A	1: 74,424,343 (GRCm39)	A434T	probably damaging	Het
Slc5a8	A	T	10: 88,722,460 (GRCm39)	I98F	possibly damaging	Het
Sorl1	T	C	9: 41,943,114 (GRCm39)	K921E	possibly damaging	Het
Stub1	A	G	17: 26,051,112 (GRCm39)	L90P	probably damaging	Het
Sycp1	A	T	3: 102,827,881 (GRCm39)	S289T	probably damaging	Het
Taar7b	T	G	10: 23,876,359 (GRCm39)	S175A	probably benign	Het
Tead3	T	C	17: 28,560,451 (GRCm39)	K51R	probably benign	Het
Tmed11	T	A	5: 108,943,089 (GRCm39)	I30L	probably benign	Het
Tmem131	A	G	1: 36,893,986 (GRCm39)	I139T	probably damaging	Het
Tmem191	A	G	16: 17,095,559 (GRCm39)	Q206R	probably null	Het
Tph2	T	A	10: 114,987,079 (GRCm39)	Y237F	probably benign	Het
Trim35	C	T	14: 66,546,421 (GRCm39)		probably benign	Het
Tsc22d1	T	C	14: 76,655,750 (GRCm39)	I661T	probably benign	Het
Ttc27	T	A	17: 75,106,337 (GRCm39)	H541Q	probably damaging	Het
Uqcrq	A	G	11: 53,320,954 (GRCm39)		probably null	Het
Vmn1r215	T	A	13: 23,260,666 (GRCm39)	S235R	probably benign	Het
Vmn1r70	T	C	7: 10,368,325 (GRCm39)	V271A	probably benign	Het
Vps13a	G	A	19: 16,631,848 (GRCm39)	R2596C	probably benign	Het
Vwa7	G	A	17: 35,243,166 (GRCm39)	V615I	probably benign	Het
Wdr90	T	C	17: 26,065,307 (GRCm39)	T1650A	probably damaging	Het
Zbtb32	T	A	7: 30,290,891 (GRCm39)	M135L	probably benign	Het
Zc2hc1c	A	G	12: 85,337,288 (GRCm39)	D315G	probably benign	Het
Zfc3h1	T	A	10: 115,254,688 (GRCm39)	C1427*	probably null	Het
Zfp30	A	G	7: 29,485,691 (GRCm39)		probably benign	Het
Zfp428	T	A	7: 24,214,550 (GRCm39)	D55E	probably damaging	Het
Zfyve26	A	T	12: 79,302,135 (GRCm39)	N1820K	probably damaging	Het
Zw10	C	A	9: 48,988,759 (GRCm39)	S675*	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
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
R7390:Gldc	UTSW	19	30,077,314 (GRCm39)	missense	possibly damaging	0.46
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'- AGTTGACACTGTCCGATTTCAC -3'
(R):5'- GTTTTGGTGAAAACACGTGGC -3'

Sequencing Primer
(F):5'- ACACTGTCCGATTTCACACCCC -3'
(R):5'- TGGCACCTAACGTGTGTCATAGAC -3'

Posted On

2016-06-06