Mutagenetix > Incidental Mutation

Incidental Mutation 'R0195:Phgdh'

23350

Institutional Source

Beutler Lab

Gene Symbol

Phgdh

Ensembl Gene

ENSMUSG00000053398

Gene Name

3-phosphoglycerate dehydrogenase

Synonyms

3PGDH, 3-PGDH, A10, PGAD, PGD, PGDH, SERA

MMRRC Submission

038454-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R0195 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

98220487-98247285 bp(-) (GRCm39)

Type of Mutation

unclassified

DNA Base Change (assembly)

T to G at 98223866 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Gene Model

predicted gene model for transcript(s): [ENSMUST00000065793]

AlphaFold

Q61753

Predicted Effect

probably benign
Transcript: ENSMUST00000065793

SMART Domains

Protein: ENSMUSP00000064755
Gene: ENSMUSG00000053398

Domain	Start	End	E-Value	Type
Pfam:2-Hacid_dh	9	317	2.1e-42	PFAM
Pfam:2-Hacid_dh_C	111	285	3.5e-60	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000148488

SMART Domains

Protein: ENSMUSP00000117525
Gene: ENSMUSG00000053398

Domain	Start	End	E-Value	Type
Pfam:2-Hacid_dh	7	145	1.1e-27	PFAM
Pfam:2-Hacid_dh_C	83	149	1.3e-21	PFAM

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000152106

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000153694

Coding Region Coverage

1x: 99.0%
3x: 98.1%
10x: 95.6%
20x: 89.4%

Validation Efficiency

98% (156/160)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes the enzyme which is involved in the early steps of L-serine synthesis in animal cells. L-serine is required for D-serine and other amino acid synthesis. The enzyme requires NAD/NADH as a cofactor and forms homotetramers for activity. Mutations in this gene have been found in a family with congenital microcephaly, psychomotor retardation and other symptoms. Multiple alternatively spliced transcript variants have been found, however the full-length nature of most are not known. [provided by RefSeq, Aug 2011]
PHENOTYPE: Mice homozygous for a null allele die by E13.5 and exhibit abnormal neural development. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 74 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Acly	C	G	11: 100,403,800 (GRCm39)	R362P	possibly damaging	Het
Adam24	T	A	8: 41,134,805 (GRCm39)	W758R	probably benign	Het
Adam26b	G	T	8: 43,973,307 (GRCm39)	T565K	probably damaging	Het
Adam7	T	G	14: 68,765,076 (GRCm39)		probably benign	Het
Adamts19	A	G	18: 59,102,942 (GRCm39)		probably benign	Het
Add1	A	G	5: 34,767,990 (GRCm39)		probably benign	Het
Ago1	A	G	4: 126,357,484 (GRCm39)	C64R	probably benign	Het
Ankrd12	C	T	17: 66,356,943 (GRCm39)		probably null	Het
Arhgef33	A	G	17: 80,688,863 (GRCm39)	K820E	probably damaging	Het
Arl9	T	C	5: 77,154,341 (GRCm39)	V8A	probably damaging	Het
Aspm	T	C	1: 139,406,873 (GRCm39)	L1920P	probably damaging	Het
Atad2	A	G	15: 57,963,350 (GRCm39)		probably benign	Het
Atp2b2	A	T	6: 113,770,835 (GRCm39)	V358E	probably benign	Het
C3ar1	A	C	6: 122,828,114 (GRCm39)	C34W	possibly damaging	Het
C6	G	A	15: 4,792,953 (GRCm39)	V353M	probably benign	Het
Capn7	T	C	14: 31,087,538 (GRCm39)	I593T	probably damaging	Het
Casc3	T	A	11: 98,712,319 (GRCm39)	D119E	probably damaging	Het
Ccna1	T	A	3: 54,961,785 (GRCm39)	E45V	probably damaging	Het
Cdc37	A	G	9: 21,053,576 (GRCm39)	V180A	probably benign	Het
Cdh23	A	G	10: 60,152,838 (GRCm39)	I2393T	probably damaging	Het
Cnbd1	T	C	4: 18,906,988 (GRCm39)		probably benign	Het
Cngb3	A	T	4: 19,280,975 (GRCm39)	M15L	probably benign	Het
Crygn	A	G	5: 24,961,036 (GRCm39)	M90T	possibly damaging	Het
Cse1l	T	A	2: 166,782,008 (GRCm39)	S661R	probably benign	Het
D830013O20Rik	C	T	12: 73,411,095 (GRCm39)		noncoding transcript	Het
Ddx24	C	T	12: 103,385,220 (GRCm39)		probably null	Het
Dnah3	A	T	7: 119,676,998 (GRCm39)		probably null	Het
Dnah9	C	T	11: 65,786,731 (GRCm39)	G3634E	probably benign	Het
Dnttip2	A	T	3: 122,069,810 (GRCm39)	T342S	probably benign	Het
Evx2	G	T	2: 74,489,388 (GRCm39)	R125S	probably damaging	Het
Fbxl5	A	T	5: 43,928,140 (GRCm39)	L40Q	probably damaging	Het
Git1	T	A	11: 77,391,899 (GRCm39)	D240E	probably benign	Het
Glp2r	T	A	11: 67,600,534 (GRCm39)	K438N	probably damaging	Het
Hivep1	T	A	13: 42,309,629 (GRCm39)	I623N	probably benign	Het
Il17re	A	G	6: 113,443,098 (GRCm39)	E312G	probably damaging	Het
Itgb7	G	A	15: 102,130,618 (GRCm39)		probably benign	Het
Itpr3	A	G	17: 27,333,088 (GRCm39)	Y1900C	probably damaging	Het
Krt1c	G	A	15: 101,721,626 (GRCm39)	Q472*	probably null	Het
Krtap5-1	A	C	7: 141,850,434 (GRCm39)	C125G	unknown	Het
Macf1	A	G	4: 123,328,709 (GRCm39)	S2554P	probably damaging	Het
Marchf10	C	T	11: 105,276,351 (GRCm39)	G646R	probably damaging	Het
Mrpl48	A	C	7: 100,195,560 (GRCm39)		probably benign	Het
Myo16	A	T	8: 10,365,538 (GRCm39)		probably benign	Het
Nrcam	A	T	12: 44,631,628 (GRCm39)	E1060D	probably benign	Het
Nsd3	T	A	8: 26,170,709 (GRCm39)	C731S	probably damaging	Het
Nup85	T	G	11: 115,455,357 (GRCm39)	M1R	probably null	Het
Nxnl2	G	T	13: 51,325,483 (GRCm39)	R42L	probably damaging	Het
Oas3	G	A	5: 120,894,210 (GRCm39)	R39C	probably damaging	Het
Or13c25	G	A	4: 52,910,849 (GRCm39)	T315M	probably benign	Het
Orc1	C	T	4: 108,471,505 (GRCm39)	R786*	probably null	Het
P2ry6	A	T	7: 100,587,904 (GRCm39)	W152R	probably damaging	Het
Pex5l	T	C	3: 33,047,102 (GRCm39)	N283D	possibly damaging	Het
Pgk2	T	C	17: 40,518,622 (GRCm39)	I269V	probably benign	Het
Pzp	A	T	6: 128,464,441 (GRCm39)	L1362Q	probably damaging	Het
Rbbp9	T	C	2: 144,390,026 (GRCm39)		probably benign	Het
Rffl	A	G	11: 82,700,989 (GRCm39)	L244P	probably damaging	Het
Serpina11	T	C	12: 103,952,131 (GRCm39)	Y213C	probably damaging	Het
Spopfm1	A	G	3: 94,173,229 (GRCm39)	Y79C	possibly damaging	Het
Srsf11	A	G	3: 157,742,172 (GRCm39)		probably benign	Het
Sspo	T	A	6: 48,463,570 (GRCm39)	V3785E	probably benign	Het
Svep1	A	T	4: 58,089,514 (GRCm39)	S1632T	possibly damaging	Het
Tm4sf1	T	A	3: 57,200,480 (GRCm39)	D74V	probably damaging	Het
Tmprss15	T	A	16: 78,831,222 (GRCm39)	T393S	probably benign	Het
Tnfaip3	A	G	10: 18,881,461 (GRCm39)	L275P	probably damaging	Het
Trim30c	A	G	7: 104,031,636 (GRCm39)	V393A	probably benign	Het
Tssk2	T	A	16: 17,717,439 (GRCm39)	S281T	probably benign	Het
Tubb4a	A	G	17: 57,388,499 (GRCm39)	S176P	probably damaging	Het
Unc45b	T	A	11: 82,828,654 (GRCm39)	M785K	probably damaging	Het
Vldlr	A	T	19: 27,215,786 (GRCm39)	D261V	probably damaging	Het
Vmn1r176	G	T	7: 23,535,010 (GRCm39)	Q48K	probably benign	Het
Vmn2r110	A	T	17: 20,794,317 (GRCm39)	L784Q	probably benign	Het
Vps13b	A	G	15: 35,472,045 (GRCm39)	T783A	probably benign	Het
Zfp800	A	G	6: 28,243,846 (GRCm39)	M373T	probably damaging	Het
Zmym1	A	G	4: 126,941,704 (GRCm39)	F895L	possibly damaging	Het

Other mutations in Phgdh

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00429:Phgdh	APN	3	98,235,631 (GRCm39)	missense	probably damaging	1.00
R0636:Phgdh	UTSW	3	98,240,607 (GRCm39)	missense	possibly damaging	0.89
R0787:Phgdh	UTSW	3	98,241,865 (GRCm39)	missense	probably damaging	1.00
R1626:Phgdh	UTSW	3	98,223,725 (GRCm39)	missense	probably benign	0.16
R1733:Phgdh	UTSW	3	98,235,451 (GRCm39)	missense	probably benign	0.00
R1782:Phgdh	UTSW	3	98,228,063 (GRCm39)	missense	probably damaging	0.97
R2173:Phgdh	UTSW	3	98,222,427 (GRCm39)	missense	probably benign	0.00
R2256:Phgdh	UTSW	3	98,235,607 (GRCm39)	missense	probably benign	0.30
R2367:Phgdh	UTSW	3	98,221,612 (GRCm39)	missense	probably benign	0.07
R2495:Phgdh	UTSW	3	98,247,105 (GRCm39)	missense	probably damaging	1.00
R4214:Phgdh	UTSW	3	98,235,377 (GRCm39)	missense	possibly damaging	0.79
R4410:Phgdh	UTSW	3	98,221,591 (GRCm39)	missense	probably benign
R5062:Phgdh	UTSW	3	98,235,655 (GRCm39)	missense	probably damaging	1.00
R5378:Phgdh	UTSW	3	98,228,639 (GRCm39)	splice site	probably null
R5528:Phgdh	UTSW	3	98,235,655 (GRCm39)	missense	probably benign	0.13
R7357:Phgdh	UTSW	3	98,247,138 (GRCm39)	missense	probably benign	0.00
R7436:Phgdh	UTSW	3	98,247,045 (GRCm39)	missense	probably benign	0.34
R7894:Phgdh	UTSW	3	98,247,124 (GRCm39)	missense	probably damaging	0.98
R8373:Phgdh	UTSW	3	98,228,561 (GRCm39)	missense	probably damaging	1.00
R8467:Phgdh	UTSW	3	98,228,627 (GRCm39)	missense	probably benign
R8762:Phgdh	UTSW	3	98,247,024 (GRCm39)	missense	possibly damaging	0.51
R9547:Phgdh	UTSW	3	98,241,950 (GRCm39)	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- CAGACCTCTGCTCACCTTGTGTAAC -3'
(R):5'- AGCCAGTACCAATGCTGCTCAATG -3'

Sequencing Primer
(F):5'- ACCTTGTGTAACCACCTGGATG -3'
(R):5'- AAGGTAGCCAGGCTTCTTAC -3'

Posted On

2013-04-16