Mutagenetix > Incidental Mutation

Incidental Mutation 'R1592:Gldc'

175698

Institutional Source

Beutler Lab

Gene Symbol

Gldc

Ensembl Gene

ENSMUSG00000024827

Gene Name

glycine decarboxylase

Synonyms

b2b2679Clo, D030049L12Rik, D19Wsu57e

MMRRC Submission

039629-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R1592 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

30075847-30152829 bp(-) (GRCm39)

Type of Mutation

intron

DNA Base Change (assembly)

G to A at 30138077 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Ref Sequence

ENSEMBL: ENSMUSP00000025778 (fasta)

Gene Model

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

AlphaFold

Q91W43

Predicted Effect

probably benign
Transcript: ENSMUST00000025778

SMART Domains

Protein: ENSMUSP00000025778
Gene: ENSMUSG00000024827

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

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000080982

Meta Mutation Damage Score

0.0898

Coding Region Coverage

1x: 99.1%
3x: 98.3%
10x: 96.1%
20x: 91.9%

Validation Efficiency

100% (51/51)

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: 43 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Acad10	T	C	5: 121,783,444 (GRCm39)	E327G	probably damaging	Het
Acp5	A	T	9: 22,039,147 (GRCm39)	W189R	probably damaging	Het
Adamts8	T	C	9: 30,854,472 (GRCm39)	S114P	probably damaging	Het
Alkbh3	A	C	2: 93,838,769 (GRCm39)		probably null	Het
Ankrd13d	T	C	19: 4,332,919 (GRCm39)	H27R	probably benign	Het
Aox1	A	G	1: 58,339,853 (GRCm39)	N382S	probably benign	Het
Aspg	G	A	12: 112,086,406 (GRCm39)	R220Q	probably benign	Het
Atg16l2	C	A	7: 100,941,193 (GRCm39)	G403V	probably damaging	Het
Bcat1	G	T	6: 144,955,784 (GRCm39)	Q299K	probably benign	Het
Cc2d1b	C	T	4: 108,483,868 (GRCm39)		probably benign	Het
Cdh26	T	C	2: 178,091,684 (GRCm39)	F81S	probably damaging	Het
Cnbd2	A	G	2: 156,177,322 (GRCm39)	I222M	probably benign	Het
Ephb3	T	C	16: 21,040,450 (GRCm39)	V562A	probably damaging	Het
Fam186a	T	C	15: 99,838,199 (GRCm39)	T2682A	probably benign	Het
Fat2	T	C	11: 55,182,696 (GRCm39)		probably null	Het
Fat4	A	T	3: 39,061,326 (GRCm39)	D4303V	probably damaging	Het
Fbln1	T	A	15: 85,115,665 (GRCm39)	S234T	probably benign	Het
Gli1	A	C	10: 127,167,198 (GRCm39)	V685G	probably damaging	Het
H2-T22	T	C	17: 36,352,469 (GRCm39)	N152S	probably damaging	Het
Inpp5d	A	T	1: 87,593,254 (GRCm39)	D118V	possibly damaging	Het
Ints10	A	G	8: 69,255,555 (GRCm39)	I182V	possibly damaging	Het
Ipcef1	C	T	10: 6,885,182 (GRCm39)		probably null	Het
Kcnj3	G	T	2: 55,327,898 (GRCm39)	R229L	probably damaging	Het
Klf11	C	A	12: 24,703,737 (GRCm39)	D57E	probably damaging	Het
Krt73	G	T	15: 101,710,674 (GRCm39)	S20*	probably null	Het
Lactbl1	A	G	4: 136,363,187 (GRCm39)		probably null	Het
Mapk10	T	C	5: 103,186,487 (GRCm39)	D45G	possibly damaging	Het
Mfrp	G	A	9: 44,014,519 (GRCm39)	C222Y	probably damaging	Het
Mga	A	T	2: 119,795,147 (GRCm39)	I2944F	possibly damaging	Het
Msh2	A	G	17: 87,987,441 (GRCm39)		probably null	Het
Nckap1l	T	A	15: 103,390,607 (GRCm39)		probably null	Het
Or5m9	A	G	2: 85,877,333 (GRCm39)	N169S	probably benign	Het
Pitpnm1	T	A	19: 4,156,964 (GRCm39)		probably null	Het
Sik2	C	T	9: 50,906,971 (GRCm39)	V85I	probably damaging	Het
Slc26a7	T	A	4: 14,552,470 (GRCm39)	E229V	probably benign	Het
Spty2d1	A	T	7: 46,648,637 (GRCm39)	D97E	possibly damaging	Het
Tcaim	G	A	9: 122,647,838 (GRCm39)		probably null	Het
Tdrd3	T	A	14: 87,743,322 (GRCm39)	N417K	probably damaging	Het
Uggt1	C	A	1: 36,241,939 (GRCm39)	A332S	probably benign	Het
Usp53	A	T	3: 122,727,699 (GRCm39)	L961*	probably null	Het
Vmn1r223	A	T	13: 23,433,837 (GRCm39)	T144S	possibly damaging	Het
Wdfy1	G	A	1: 79,683,972 (GRCm39)	R388C	probably damaging	Het
Zfp995	T	A	17: 22,106,321 (GRCm39)	M1L	probably damaging	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
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
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'- ACCAGTTAACACCAGAGTCCAGGAG -3'
(R):5'- CGCGTAAGTTACCAGCGTGTAGAG -3'

Sequencing Primer
(F):5'- gtgtctcctaaaacaatacatttgc -3'
(R):5'- TACTCGGCTGCGATATGGAAC -3'

Posted On

2014-04-24