Mutagenetix > Incidental Mutation

Incidental Mutation 'R8374:Gldc'

646603

Institutional Source

Beutler Lab

Gene Symbol

Gldc

Ensembl Gene

ENSMUSG00000024827

Gene Name

glycine decarboxylase

Synonyms

b2b2679Clo, D030049L12Rik, D19Wsu57e

MMRRC Submission

067742-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R8374 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

30075847-30152829 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to C at 30114594 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Phenylalanine to Valine at position 439 (F439V)

Ref Sequence

ENSEMBL: ENSMUSP00000025778 (fasta)

Gene Model

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

AlphaFold

Q91W43

Predicted Effect

probably damaging
Transcript: ENSMUST00000025778
AA Change: F439V

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

SMART Domains

Protein: ENSMUSP00000025778
Gene: ENSMUSG00000024827
AA Change: F439V

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: 100.0%
10x: 99.8%
20x: 99.5%

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: 43 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Adamts15	C	T	9: 30,814,002 (GRCm39)	G721E	probably benign	Het
Aip	A	T	19: 4,165,456 (GRCm39)	M170K	probably damaging	Het
Alms1	T	C	6: 85,585,973 (GRCm39)	I276T	probably benign	Het
Arid1b	C	T	17: 5,392,919 (GRCm39)	P2097S	possibly damaging	Het
Astn1	T	G	1: 158,329,803 (GRCm39)	N219K	probably damaging	Het
Cbx2	G	T	11: 118,918,969 (GRCm39)	R178L	probably damaging	Het
Clptm1	G	A	7: 19,372,081 (GRCm39)	P252S	probably benign	Het
Crebbp	A	G	16: 3,902,175 (GRCm39)	S2355P	probably damaging	Het
D130043K22Rik	C	A	13: 25,041,962 (GRCm39)	T297K	probably benign	Het
Ddx60	A	G	8: 62,427,205 (GRCm39)	D760G	probably benign	Het
Dgka	T	C	10: 128,557,112 (GRCm39)	N621S	probably benign	Het
Ear10	A	T	14: 44,160,645 (GRCm39)	C61S	probably damaging	Het
F12	A	T	13: 55,569,144 (GRCm39)	C238S	probably damaging	Het
Fen1	A	G	19: 10,177,824 (GRCm39)	F207L	probably benign	Het
Fzr1	A	G	10: 81,203,368 (GRCm39)	L486P	probably damaging	Het
Gdnf	A	G	15: 7,864,176 (GRCm39)	R196G	probably benign	Het
Gm3138	T	C	14: 4,251,688 (GRCm38)	M120T	probably damaging	Het
Gpi1	G	A	7: 33,920,082 (GRCm39)	A197V	probably benign	Het
Ighv1-4	T	A	12: 114,450,899 (GRCm39)	I70F	probably benign	Het
Il19	A	T	1: 130,866,893 (GRCm39)	L29Q	probably damaging	Het
Kank1	A	T	19: 25,389,005 (GRCm39)	I893F	probably damaging	Het
Kcnq5	G	A	1: 21,549,648 (GRCm39)	R360C	probably damaging	Het
Kif13b	T	C	14: 65,025,884 (GRCm39)	S1414P	probably damaging	Het
Miga2	AAGAG	AAG	2: 30,265,755 (GRCm39)		probably null	Het
Mosmo	T	A	7: 120,329,715 (GRCm39)	M112K	probably benign	Het
Ntmt2	A	T	1: 163,530,617 (GRCm39)	M274K	probably damaging	Het
Or2d2b	A	G	7: 106,706,033 (GRCm39)	F12L	probably damaging	Het
Or2h1b	C	A	17: 37,462,636 (GRCm39)	V76F	probably damaging	Het
Or2w3b	T	A	11: 58,623,724 (GRCm39)	D89V	probably damaging	Het
Pak6	G	A	2: 118,524,477 (GRCm39)	V497I	probably benign	Het
Ppargc1b	G	A	18: 61,443,564 (GRCm39)	S549F	probably damaging	Het
Rassf8	T	A	6: 145,760,863 (GRCm39)	L63*	probably null	Het
Rptn	G	T	3: 93,303,602 (GRCm39)	G312*	probably null	Het
Rsph14	T	C	10: 74,797,481 (GRCm39)	I169V	probably benign	Het
Sltm	A	G	9: 70,469,227 (GRCm39)	D162G	probably null	Het
Tatdn1	C	T	15: 58,788,000 (GRCm39)		probably null	Het
Tbx4	A	C	11: 85,805,102 (GRCm39)	E397A	probably benign	Het
Tdrd12	T	C	7: 35,177,486 (GRCm39)	D956G	unknown	Het
Tnr	G	A	1: 159,685,953 (GRCm39)	V395I	probably benign	Het
Ugt1a2	A	T	1: 88,129,107 (GRCm39)	H250L	possibly damaging	Het
Vmn1r173	C	T	7: 23,401,920 (GRCm39)	H52Y	probably damaging	Het
Vps11	T	C	9: 44,267,706 (GRCm39)	D302G	probably benign	Het
Zfp398	T	C	6: 47,836,468 (GRCm39)		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
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
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'- CTGAGGACAATCTGCTTCTTTG -3'
(R):5'- ACAATGAGATTGCACCCATTTC -3'

Sequencing Primer
(F):5'- GAGGACAATCTGCTTCTTTGAAAAG -3'
(R):5'- TGAGATTGCACCCATTTCTAATATG -3'

Posted On

2020-09-02