Mutagenetix > Incidental Mutations

Incidental Mutation 'R8171:Gldc'

634168

Institutional Source

Beutler Lab

Gene Symbol

Gldc

Ensembl Gene

ENSMUSG00000024827

Gene Name

glycine decarboxylase

Synonyms

D030049L12Rik, D19Wsu57e

MMRRC Submission

Accession Numbers

Genbank: NM_138595.1

Is this an essential gene?

Essential (E-score: 1.000) question?

Stock #

R8171 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

30098449-30175418 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

A to T at 30133761 bp

Zygosity

Heterozygous

Amino Acid Change

Asparagine to Lysine at position 538 (N538K)

Ref Sequence

ENSEMBL: ENSMUSP00000025778 (fasta)

Gene Model

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

Predicted Effect

probably benign
Transcript: ENSMUST00000025778
AA Change: N538K

PolyPhen 2 Score 0.240 (Sensitivity: 0.91; Specificity: 0.88)

SMART Domains

Protein: ENSMUSP00000025778
Gene: ENSMUSG00000024827
AA Change: N538K

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: 99.4%
20x: 97.9%

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: 95 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
3425401B19Rik	G	T	14: 32,662,025	A661E	probably benign	Het
4932438A13Rik	T	C	3: 36,975,713	V2423A	probably benign	Het
4933425L06Rik	T	A	13: 105,109,783	V284E	probably benign	Het
Abhd14a	T	A	9: 106,440,761	T142S	probably benign	Het
Actn1	A	G	12: 80,196,393		probably null	Het
Adss	T	C	1: 177,796,351	N15S	probably benign	Het
Alpk2	A	G	18: 65,305,983	S780P	probably benign	Het
Asap1	G	T	15: 64,110,966	L830M	probably damaging	Het
Atic	T	C	1: 71,569,873	V319A	possibly damaging	Het
Atp8a2	A	T	14: 60,046,044	I87N	probably damaging	Het
Bace2	G	T	16: 97,424,586	V407L	possibly damaging	Het
Bmp3	A	T	5: 98,872,669	Y317F	probably damaging	Het
Ccdc159	A	G	9: 21,933,711	E291G	possibly damaging	Het
Cct8l1	T	A	5: 25,516,554	L89Q	probably damaging	Het
Cep83	T	A	10: 94,768,935	N503K	possibly damaging	Het
Ces4a	A	G	8: 105,147,207	Y436C	probably damaging	Het
Cftr	T	A	6: 18,258,288	D579E	probably damaging	Het
Chd9	T	A	8: 91,025,387	V1751D	possibly damaging	Het
Clasp2	A	T	9: 113,903,906	T937S	possibly damaging	Het
Clock	T	A	5: 76,266,414	D17V	possibly damaging	Het
Cpm	T	C	10: 117,683,315	L376P	probably damaging	Het
Crocc2	T	C	1: 93,189,001		probably null	Het
Csnk1g2	A	G	10: 80,639,802	D401G	probably damaging	Het
Cyb5r4	C	T	9: 87,042,810	L206F	possibly damaging	Het
Cyp1a1	T	A	9: 57,700,196	W36R	probably benign	Het
Cyp3a59	A	T	5: 146,085,774	H30L	probably damaging	Het
Dab2	G	A	15: 6,423,926	V182I	probably benign	Het
Dnah1	G	T	14: 31,297,110	F1342L	probably damaging	Het
Draxin	A	T	4: 148,115,666	L109Q	possibly damaging	Het
Elfn1	G	A	5: 139,971,357	V39M	probably damaging	Het
Erlin1	A	G	19: 44,069,329	I19T	probably benign	Het
F830016B08Rik	T	A	18: 60,300,078	S78T	possibly damaging	Het
Fer1l4	A	G	2: 156,048,231	V258A	probably benign	Het
Fgb	T	C	3: 83,042,515	D445G	probably damaging	Het
Fgd6	T	C	10: 94,074,332		probably null	Het
Frem3	T	A	8: 80,615,240	D1387E	probably damaging	Het
Gdf3	T	C	6: 122,609,903	T22A	probably benign	Het
Glcci1	C	T	6: 8,593,167	A511V	probably benign	Het
Glipr1l1	C	T	10: 112,078,384	P217S	probably benign	Het
Gm15800	A	G	5: 121,318,756	E728G	possibly damaging	Het
Gm35339	C	A	15: 76,363,619	F1614L		Het
Gpr161	A	G	1: 165,306,436	N89S	probably damaging	Het
Gypa	T	A	8: 80,509,463	S166T	probably benign	Het
Hcar1	A	G	5: 123,879,089	S180P	probably damaging	Het
Hcn1	T	C	13: 117,602,734	S11P	unknown	Het
Itih1	A	T	14: 30,937,090	M323K	possibly damaging	Het
Ivl	A	G	3: 92,571,778	S327P	probably damaging	Het
Kcnt2	T	A	1: 140,509,465	N545K	probably benign	Het
Kdm4b	A	T	17: 56,389,534	R417W	probably damaging	Het
Kif13a	T	C	13: 46,778,968	E1083G	probably damaging	Het
Klhl40	A	T	9: 121,778,557	H261L	probably benign	Het
Kpnb1	A	G	11: 97,175,747		probably null	Het
Lamc3	C	A	2: 31,914,971	T621N	probably benign	Het
Lingo3	T	C	10: 80,834,761	H445R	probably benign	Het
Ly75	G	A	2: 60,314,228	T1297I	possibly damaging	Het
Lypd6	C	T	2: 50,190,747	T149M	possibly damaging	Het
Mcrs1	A	T	15: 99,248,732	D139E	probably damaging	Het
Muc5b	G	A	7: 141,861,000	S2561N	unknown	Het
Mybpc1	C	T	10: 88,523,003	G1095R	probably damaging	Het
Myh1	A	G	11: 67,202,572	Y163C	probably damaging	Het
Notch4	T	A	17: 34,582,509	C1110*	probably null	Het
Olfr1257	A	G	2: 89,881,065	I80V	probably benign	Het
Olfr527	A	T	7: 140,336,230	I123F	probably damaging	Het
Olfr705	T	A	7: 106,714,619	S21C		Het
Olfr705	C	T	7: 106,714,618	S21N	probably benign	Het
Pcsk1	T	A	13: 75,090,091	C10*	probably null	Het
Pdlim5	A	T	3: 142,312,187	S107T	probably benign	Het
Plac8l1	T	A	18: 42,180,380	D99V	probably damaging	Het
Plin2	A	T	4: 86,657,112	V400E	probably damaging	Het
Plxna1	G	A	6: 89,357,120	P176S	probably benign	Het
Pnn	A	G	12: 59,070,437	K238R	probably damaging	Het
Pou5f1	A	G	17: 35,510,036	E231G	probably benign	Het
Ppara	A	T	15: 85,797,876	M258L	probably benign	Het
Prune2	G	A	19: 17,120,518	D1129N	probably damaging	Het
Rai14	G	A	15: 10,633,163	T47M	probably damaging	Het
Rdh5	T	C	10: 128,918,100	I117V	probably benign	Het
Rpain	G	A	11: 70,973,898	C137Y	probably damaging	Het
Scn3a	A	G	2: 65,530,810	V126A	possibly damaging	Het
Senp7	G	T	16: 56,111,726	L129F	probably damaging	Het
Setd1a	A	G	7: 127,791,227	D1025G	unknown	Het
Sirt4	A	T	5: 115,483,023	V30E	probably damaging	Het
Slit1	C	A	19: 41,727,073	R113L	probably damaging	Het
Stxbp5l	G	A	16: 37,208,054	T549I	noncoding transcript	Het
Sytl2	A	G	7: 90,409,470	M926V	probably damaging	Het
Tgfbr2	C	T	9: 116,130,006	W113*	probably null	Het
Tmem86a	A	G	7: 47,053,764	Y213C	probably damaging	Het
Tpo	T	A	12: 30,104,046	Y220F	probably damaging	Het
Ttc6	C	A	12: 57,673,310	A889E	probably damaging	Het
Tyw1	A	G	5: 130,300,014	D547G	probably benign	Het
Ubtfl1	A	G	9: 18,409,227	K17R	probably benign	Het
Usp46	T	A	5: 74,002,693	I331F	probably benign	Het
Vmn2r111	T	C	17: 22,573,092	H61R	probably benign	Het
Vwa9	A	T	9: 64,973,250	H213L	possibly damaging	Het
Wdr75	T	A	1: 45,822,546	N715K	probably benign	Het
Zfp772	A	T	7: 7,204,097	C198*	probably null	Het

Other mutations in Gldc

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00160:Gldc	APN	19	30115240	missense	probably damaging	1.00
IGL01016:Gldc	APN	19	30133493	missense	possibly damaging	0.93
IGL01112:Gldc	APN	19	30158513	critical splice donor site	probably null
IGL01510:Gldc	APN	19	30113721	critical splice donor site	probably null
IGL01516:Gldc	APN	19	30099032	missense	probably damaging	1.00
IGL01598:Gldc	APN	19	30133756	missense	probably damaging	1.00
IGL01646:Gldc	APN	19	30100765	missense	possibly damaging	0.61
IGL02024:Gldc	APN	19	30100827	missense	probably damaging	1.00
IGL02125:Gldc	APN	19	30147241	missense	probably benign	0.03
IGL02548:Gldc	APN	19	30099899	missense	probably benign
IGL02711:Gldc	APN	19	30145146	critical splice donor site	probably null
IGL02818:Gldc	APN	19	30136509	missense	probably damaging	0.99
IGL02982:Gldc	APN	19	30145145	critical splice donor site	probably null
IGL03165:Gldc	APN	19	30098993	missense	possibly damaging	0.61
jojoba	UTSW	19	30133512	missense	probably damaging	1.00
miserable	UTSW	19	30151536	missense	probably damaging	1.00
Urchin	UTSW	19	30118602	missense	probably damaging	0.98
I2289:Gldc	UTSW	19	30147176	nonsense	probably null
R0180:Gldc	UTSW	19	30100817	missense	possibly damaging	0.95
R0269:Gldc	UTSW	19	30118602	missense	probably damaging	0.98
R0277:Gldc	UTSW	19	30116451	missense	possibly damaging	0.84
R1085:Gldc	UTSW	19	30151428	missense	probably damaging	1.00
R1159:Gldc	UTSW	19	30160762	intron	probably benign
R1500:Gldc	UTSW	19	30113825	missense	possibly damaging	0.88
R1507:Gldc	UTSW	19	30118638	missense	probably damaging	1.00
R1592:Gldc	UTSW	19	30160677	intron	probably benign
R1593:Gldc	UTSW	19	30113750	missense	probably damaging	1.00
R1675:Gldc	UTSW	19	30143453	missense	probably damaging	1.00
R1869:Gldc	UTSW	19	30139332	missense	probably benign
R1965:Gldc	UTSW	19	30137113	nonsense	probably null
R2312:Gldc	UTSW	19	30100826	missense	probably damaging	0.98
R2425:Gldc	UTSW	19	30131790	missense	probably damaging	1.00
R3836:Gldc	UTSW	19	30118675	splice site	probably benign
R3837:Gldc	UTSW	19	30118675	splice site	probably benign
R3839:Gldc	UTSW	19	30118675	splice site	probably benign
R4191:Gldc	UTSW	19	30145658	missense	probably damaging	0.96
R4380:Gldc	UTSW	19	30160768	intron	probably benign
R4508:Gldc	UTSW	19	30143407	missense	probably damaging	1.00
R4570:Gldc	UTSW	19	30174439	missense	probably benign
R4655:Gldc	UTSW	19	30160702	intron	probably benign
R4842:Gldc	UTSW	19	30133732	missense	possibly damaging	0.94
R5070:Gldc	UTSW	19	30118598	missense	possibly damaging	0.84
R5085:Gldc	UTSW	19	30151536	missense	probably damaging	1.00
R5268:Gldc	UTSW	19	30145725	missense	probably damaging	0.96
R5368:Gldc	UTSW	19	30158521	missense	probably benign
R5718:Gldc	UTSW	19	30110772	nonsense	probably null
R5878:Gldc	UTSW	19	30143467	splice site	probably null
R6192:Gldc	UTSW	19	30133772	missense	probably damaging	0.98
R6453:Gldc	UTSW	19	30116517	missense	probably damaging	0.99
R6777:Gldc	UTSW	19	30133512	missense	probably damaging	1.00
R6865:Gldc	UTSW	19	30133762	missense	possibly damaging	0.92
R7332:Gldc	UTSW	19	30116526	missense	probably damaging	0.99
R7390:Gldc	UTSW	19	30099914	missense	possibly damaging	0.46
R7647:Gldc	UTSW	19	30118667	missense	probably damaging	0.96
R8081:Gldc	UTSW	19	30158587	frame shift	probably null
R8321:Gldc	UTSW	19	30143407	nonsense	probably null
R8374:Gldc	UTSW	19	30137194	missense	probably damaging	1.00
R8503:Gldc	UTSW	19	30099854	missense	probably benign	0.26
R8510:Gldc	UTSW	19	30116505	missense	probably damaging	1.00
R8785:Gldc	UTSW	19	30115234	missense	probably damaging	1.00
R8818:Gldc	UTSW	19	30100812	missense	probably benign	0.05
R8820:Gldc	UTSW	19	30100812	missense	probably benign	0.05
R8829:Gldc	UTSW	19	30100812	missense	probably benign	0.05
R8830:Gldc	UTSW	19	30100812	missense	probably benign	0.05
R8859:Gldc	UTSW	19	30139379	missense	probably damaging	1.00
Z1177:Gldc	UTSW	19	30110778	missense	probably damaging	1.00
Z1177:Gldc	UTSW	19	30110779	missense	probably damaging	0.99
Z1177:Gldc	UTSW	19	30145748	missense	possibly damaging	0.61

Predicted Primers

PCR Primer
(F):5'- GGCTATGCCCCATCTATGAACC -3'
(R):5'- TTCATCTCAGGAACCCCGTGTC -3'

Sequencing Primer
(F):5'- ATGCCCCATCTATGAACCTTCCC -3'
(R):5'- AGGAACCCCGTGTCCTCTTC -3'

Posted On

2020-07-13