Mutagenetix > Incidental Mutation

Incidental Mutation 'R0277:Gldc'

24436

Institutional Source

Beutler Lab

Gene Symbol

Gldc

Ensembl Gene

ENSMUSG00000024827

Gene Name

glycine decarboxylase

Synonyms

b2b2679Clo, D030049L12Rik, D19Wsu57e

MMRRC Submission

038499-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R0277 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

30075847-30152829 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 30093851 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Isoleucine to Threonine at position 722 (I722T)

Ref Sequence

ENSEMBL: ENSMUSP00000025778 (fasta)

Gene Model

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

AlphaFold

Q91W43

Predicted Effect

possibly damaging
Transcript: ENSMUST00000025778
AA Change: I722T

PolyPhen 2 Score 0.843 (Sensitivity: 0.83; Specificity: 0.93)

SMART Domains

Protein: ENSMUSP00000025778
Gene: ENSMUSG00000024827
AA Change: I722T

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

Meta Mutation Damage Score

0.8551

Coding Region Coverage

1x: 98.8%
3x: 97.7%
10x: 95.0%
20x: 89.3%

Validation Efficiency

99% (111/112)

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: 109 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4930533L02Rik	A	G	7: 124,917,815 (GRCm39)	K69R	unknown	Het
Abca13	A	C	11: 9,244,701 (GRCm39)	D2188A	probably benign	Het
Acad11	T	C	9: 104,001,224 (GRCm39)	M708T	probably damaging	Het
Adam7	T	C	14: 68,748,306 (GRCm39)		probably null	Het
Adgre1	T	A	17: 57,751,060 (GRCm39)	I578N	probably benign	Het
Agbl4	T	C	4: 111,474,419 (GRCm39)	S403P	probably damaging	Het
Ak3	A	G	19: 29,025,192 (GRCm39)	M13T	possibly damaging	Het
Ap2s1	T	C	7: 16,481,305 (GRCm39)		probably benign	Het
Arhgef1	A	T	7: 24,623,224 (GRCm39)		probably benign	Het
Arsk	T	C	13: 76,223,051 (GRCm39)	N182S	probably benign	Het
Aspscr1	G	A	11: 120,569,246 (GRCm39)	V15I	probably damaging	Het
Asxl2	A	G	12: 3,492,487 (GRCm39)	Y24C	probably damaging	Het
Atp8b1	A	G	18: 64,701,323 (GRCm39)	F345S	possibly damaging	Het
Atp8b3	T	C	10: 80,362,743 (GRCm39)	K672E	probably benign	Het
Bltp1	T	A	3: 36,997,331 (GRCm39)	C1129*	probably null	Het
Bmp2k	A	G	5: 97,235,682 (GRCm39)		probably benign	Het
Casp6	T	A	3: 129,704,172 (GRCm39)	V86E	probably benign	Het
Cdca5	A	G	19: 6,140,742 (GRCm39)	E260G	unknown	Het
Cpb2	T	A	14: 75,502,898 (GRCm39)	V159D	probably damaging	Het
Cylc2	T	A	4: 51,228,477 (GRCm39)	S183T	unknown	Het
Dhtkd1	T	A	2: 5,919,699 (GRCm39)	M561L	probably benign	Het
Dync2h1	T	C	9: 7,129,046 (GRCm39)	D1823G	probably benign	Het
Efcab5	G	A	11: 77,031,749 (GRCm39)	R42W	probably damaging	Het
Erc1	T	C	6: 119,597,289 (GRCm39)	K1003E	probably damaging	Het
Ezr	G	A	17: 7,022,164 (GRCm39)	Q105*	probably null	Het
Fam83d	T	A	2: 158,627,467 (GRCm39)	D385E	probably benign	Het
Fbn2	A	G	18: 58,178,389 (GRCm39)	C1950R	probably damaging	Het
Fbxo32	A	T	15: 58,047,605 (GRCm39)	I236N	probably damaging	Het
Fcgbp	G	T	7: 27,784,918 (GRCm39)		probably null	Het
Foxe3	T	C	4: 114,782,805 (GRCm39)	N136D	probably damaging	Het
Fscn2	A	T	11: 120,258,837 (GRCm39)	I461F	probably damaging	Het
Gm10717	T	G	9: 3,025,619 (GRCm39)	V68G	possibly damaging	Het
Gm4841	A	G	18: 60,403,718 (GRCm39)	L125S	possibly damaging	Het
Gnl3	A	C	14: 30,735,384 (GRCm39)		probably null	Het
Gsto1	A	T	19: 47,846,416 (GRCm39)	I88F	probably damaging	Het
Gucy1b1	T	A	3: 81,945,463 (GRCm39)		probably null	Het
Hhla1	C	A	15: 65,820,352 (GRCm39)	V133F	probably benign	Het
Hipk3	T	A	2: 104,271,593 (GRCm39)	L446F	probably damaging	Het
Hscb	T	C	5: 110,982,556 (GRCm39)	E177G	possibly damaging	Het
Hsd17b6	T	C	10: 127,827,274 (GRCm39)	D266G	probably benign	Het
Ipo4	T	C	14: 55,869,572 (GRCm39)	S363G	probably benign	Het
Kcnip3	A	G	2: 127,301,899 (GRCm39)		probably benign	Het
Klhl41	A	G	2: 69,501,640 (GRCm39)	Y367C	probably damaging	Het
Klk1b4	C	G	7: 43,861,053 (GRCm39)	P232R	possibly damaging	Het
Lcp2	A	G	11: 34,004,322 (GRCm39)	D53G	probably damaging	Het
Llgl2	A	G	11: 115,741,546 (GRCm39)	K559E	probably damaging	Het
Lrrc59	A	C	11: 94,534,248 (GRCm39)	T269P	probably damaging	Het
Mark1	A	G	1: 184,677,149 (GRCm39)	S34P	possibly damaging	Het
Megf11	G	A	9: 64,598,632 (GRCm39)		probably null	Het
Mplkip	A	G	13: 17,871,565 (GRCm39)	I159V	possibly damaging	Het
Muc4	C	A	16: 32,755,690 (GRCm38)		probably benign	Het
Myo18b	A	G	5: 112,841,213 (GRCm39)		probably benign	Het
Myo9b	T	C	8: 71,808,596 (GRCm39)		probably benign	Het
Napg	C	T	18: 63,120,034 (GRCm39)	R149C	probably damaging	Het
Ndrg3	A	G	2: 156,776,855 (GRCm39)		probably benign	Het
Nfe2l3	T	A	6: 51,434,448 (GRCm39)	M336K	probably benign	Het
Nrxn1	A	C	17: 91,008,170 (GRCm39)		probably null	Het
Nsun3	A	T	16: 62,597,007 (GRCm39)		probably benign	Het
Nuak1	T	C	10: 84,210,315 (GRCm39)	E591G	probably benign	Het
Or10g1b	T	C	14: 52,627,846 (GRCm39)	Y128C	probably damaging	Het
Or10s1	G	A	9: 39,986,010 (GRCm39)	V140I	probably benign	Het
Or1e17	A	T	11: 73,831,773 (GRCm39)	I234F	probably benign	Het
Or4k2	T	C	14: 50,423,789 (GRCm39)	N296S	probably null	Het
Or6c70	T	A	10: 129,709,936 (GRCm39)	Q230L	probably damaging	Het
Or6d15	A	T	6: 116,559,562 (GRCm39)	V115E	probably damaging	Het
Or6z6	T	A	7: 6,491,433 (GRCm39)	M147L	probably benign	Het
Orc4	A	T	2: 48,827,479 (GRCm39)	V38E	possibly damaging	Het
Ovgp1	T	C	3: 105,887,208 (GRCm39)		probably benign	Het
Palm3	T	A	8: 84,755,349 (GRCm39)	V287D	probably damaging	Het
Pde4dip	T	A	3: 97,751,028 (GRCm39)	H62L	probably benign	Het
Pdk4	G	T	6: 5,491,620 (GRCm39)	P100Q	probably damaging	Het
Pdss2	T	A	10: 43,248,172 (GRCm39)	H225Q	probably benign	Het
Pkhd1	A	T	1: 20,345,762 (GRCm39)	D2755E	probably benign	Het
Prune2	A	T	19: 17,098,753 (GRCm39)	D1419V	probably damaging	Het
Pth2r	A	C	1: 65,427,775 (GRCm39)	I483L	probably benign	Het
Qrsl1	A	G	10: 43,772,003 (GRCm39)		probably null	Het
Rab11fip4	A	G	11: 79,577,455 (GRCm39)	H403R	possibly damaging	Het
Ralgapa1	A	T	12: 55,724,023 (GRCm39)	I1548N	probably damaging	Het
Ric8a	T	G	7: 140,437,813 (GRCm39)		probably benign	Het
Rsbn1	T	C	3: 103,821,897 (GRCm39)	F44S	possibly damaging	Het
Serpinc1	T	A	1: 160,817,272 (GRCm39)	M1K	probably null	Het
Sf3b1	T	C	1: 55,058,416 (GRCm39)	I58V	probably damaging	Het
Sh3d19	T	A	3: 86,033,978 (GRCm39)	M777K	probably benign	Het
Sipa1	A	T	19: 5,704,093 (GRCm39)	M743K	probably benign	Het
Skint5	T	C	4: 113,794,818 (GRCm39)	H255R	probably benign	Het
Slco6b1	A	T	1: 96,916,398 (GRCm39)		noncoding transcript	Het
Slfn4	A	T	11: 83,077,777 (GRCm39)	R188S	probably damaging	Het
Sort1	T	C	3: 108,231,908 (GRCm39)		probably benign	Het
Spg21	A	T	9: 65,372,629 (GRCm39)	K20N	possibly damaging	Het
Sptbn2	A	T	19: 4,795,173 (GRCm39)	I1544F	probably benign	Het
Srf	T	C	17: 46,860,415 (GRCm39)	T456A	possibly damaging	Het
Ssbp2	T	A	13: 91,712,715 (GRCm39)		probably benign	Het
Stx2	C	T	5: 129,065,967 (GRCm39)	V230I	probably benign	Het
Sv2b	A	T	7: 74,856,187 (GRCm39)	D34E	possibly damaging	Het
Synpo2l	A	G	14: 20,711,856 (GRCm39)	S255P	probably damaging	Het
Tbx15	C	T	3: 99,259,707 (GRCm39)	P526L	probably damaging	Het
Tenm4	C	A	7: 96,344,157 (GRCm39)	P250Q	possibly damaging	Het
Tgm1	C	A	14: 55,948,384 (GRCm39)		probably benign	Het
Tgm1	T	C	14: 55,950,109 (GRCm39)		probably benign	Het
Thsd7b	A	G	1: 130,123,000 (GRCm39)	I1540V	probably benign	Het
Tnrc6c	A	G	11: 117,630,707 (GRCm39)	K1023E	probably damaging	Het
Ube2l6	A	T	2: 84,636,771 (GRCm39)		probably null	Het
Uty	T	A	Y: 1,169,979 (GRCm39)	I326F	probably damaging	Het
Wdfy4	T	C	14: 32,805,742 (GRCm39)	D1735G	possibly damaging	Het
Wnt11	A	G	7: 98,496,590 (GRCm39)	K177E	probably damaging	Het
Wnt5a	A	T	14: 28,235,225 (GRCm39)	M70L	possibly damaging	Het
Wwc1	T	A	11: 35,743,175 (GRCm39)	E882V	probably damaging	Het
Zfp455	G	T	13: 67,346,728 (GRCm39)		probably null	Het
Zmpste24	A	G	4: 120,940,050 (GRCm39)	Y199H	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
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
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'- AACTGAGAACTTGCCAGGTCATGTC -3'
(R):5'- CCTAAAAGGGCTTTGCTGCTGC -3'

Sequencing Primer
(F):5'- TCATGTCCCCGGAGGAATG -3'
(R):5'- CAGTTGTAGACTGAGATATTGTCAAG -3'

Posted On

2013-04-16