Mutagenetix > Incidental Mutation

Incidental Mutation 'R0636:Phgdh'

56659

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

038825-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R0636 (G1)

Quality Score

219

Status

Validated

Chromosome

Chromosomal Location

98220487-98247285 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

G to T at 98240607 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Asparagine to Lysine at position 100 (N100K)

Ref Sequence

ENSEMBL: ENSMUSP00000064755 (fasta)

Gene Model

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

AlphaFold

Q61753

Predicted Effect

possibly damaging
Transcript: ENSMUST00000065793
AA Change: N100K

PolyPhen 2 Score 0.891 (Sensitivity: 0.82; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000064755
Gene: ENSMUSG00000053398
AA Change: N100K

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

unknown
Transcript: ENSMUST00000148488
AA Change: N71K

SMART Domains

Protein: ENSMUSP00000117525
Gene: ENSMUSG00000053398
AA Change: N71K

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

Meta Mutation Damage Score

0.1795

Coding Region Coverage

1x: 99.4%
3x: 98.9%
10x: 97.7%
20x: 95.7%

Validation Efficiency

96% (74/77)

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
4921539E11Rik	T	C	4: 103,088,414 (GRCm39)	Y264C	probably damaging	Het
8030423J24Rik	T	C	13: 71,032,344 (GRCm39)	F139L	unknown	Het
Aco1	A	G	4: 40,175,697 (GRCm39)	E146G	probably damaging	Het
Adam2	T	G	14: 66,272,265 (GRCm39)	D639A	probably benign	Het
Adh4	G	T	3: 138,133,835 (GRCm39)	R315L	probably damaging	Het
Adprhl1	T	C	8: 13,298,702 (GRCm39)	D76G	probably damaging	Het
Akip1	T	C	7: 109,306,726 (GRCm39)		probably benign	Het
Ap3d1	T	A	10: 80,555,216 (GRCm39)	K370*	probably null	Het
Arfgef1	C	A	1: 10,270,076 (GRCm39)	V358L	probably benign	Het
Arpp21	A	T	9: 112,012,566 (GRCm39)	D85E	probably benign	Het
Azi2	A	T	9: 117,891,125 (GRCm39)	L383F	probably benign	Het
Bpgm	T	A	6: 34,481,222 (GRCm39)	D206E	probably benign	Het
Bsn	T	C	9: 107,985,033 (GRCm39)	D3007G	unknown	Het
Ccdc142	T	G	6: 83,084,179 (GRCm39)		probably benign	Het
Cep135	T	C	5: 76,763,504 (GRCm39)	V498A	probably benign	Het
Cntn6	A	T	6: 104,840,109 (GRCm39)	Q1003L	probably benign	Het
Cntnap2	T	A	6: 47,273,642 (GRCm39)		probably benign	Het
Csf2rb2	G	A	15: 78,176,160 (GRCm39)	Q139*	probably null	Het
Cyp3a16	A	G	5: 145,399,895 (GRCm39)	V101A	probably benign	Het
D630045J12Rik	T	C	6: 38,173,713 (GRCm39)	T152A	probably benign	Het
Def8	G	A	8: 124,181,096 (GRCm39)	W176*	probably null	Het
Dgkg	A	G	16: 22,398,479 (GRCm39)		probably benign	Het
Ear10	T	C	14: 44,160,451 (GRCm39)		probably null	Het
Fbxw2	A	T	2: 34,712,859 (GRCm39)	Y67*	probably null	Het
Flii	T	A	11: 60,606,378 (GRCm39)	Y1104F	probably damaging	Het
Gm973	G	A	1: 59,590,303 (GRCm39)	R270K	probably benign	Het
Gnl3	T	A	14: 30,739,110 (GRCm39)	K75N	probably damaging	Het
Gpc6	A	T	14: 117,861,905 (GRCm39)	M274L	probably benign	Het
Ifi47	A	G	11: 48,987,478 (GRCm39)	E415G	possibly damaging	Het
Ift57	A	G	16: 49,532,259 (GRCm39)	T130A	probably benign	Het
Itpr2	T	A	6: 146,072,910 (GRCm39)	D2373V	probably damaging	Het
Kat6a	T	C	8: 23,429,339 (GRCm39)	S1565P	possibly damaging	Het
Klhl6	A	T	16: 19,766,823 (GRCm39)		probably benign	Het
Klra2	T	C	6: 131,197,067 (GRCm39)		probably benign	Het
Lama5	A	G	2: 179,831,124 (GRCm39)		probably null	Het
Mapk4	A	G	18: 74,063,525 (GRCm39)	S566P	probably benign	Het
Mindy4	C	A	6: 55,253,570 (GRCm39)	R480S	possibly damaging	Het
Mterf3	T	C	13: 67,070,817 (GRCm39)		probably benign	Het
Mtmr2	A	G	9: 13,713,209 (GRCm39)		probably null	Het
Myef2l	T	C	3: 10,153,843 (GRCm39)	L204P	possibly damaging	Het
Naip5	T	C	13: 100,356,196 (GRCm39)	T1140A	probably benign	Het
Nf1	A	G	11: 79,426,529 (GRCm39)	T1648A	probably damaging	Het
Nlk	A	T	11: 78,586,670 (GRCm39)	D141E	probably benign	Het
Noxa1	C	A	2: 24,976,106 (GRCm39)		probably benign	Het
Or4g16	A	G	2: 111,136,757 (GRCm39)	N69S	probably benign	Het
Or5b121	A	T	19: 13,507,613 (GRCm39)	Y236F	possibly damaging	Het
Or5p55	T	C	7: 107,566,679 (GRCm39)	V25A	probably benign	Het
Otog	G	A	7: 45,913,652 (GRCm39)		probably null	Het
Pebp4	T	C	14: 70,285,796 (GRCm39)		probably benign	Het
Pnisr	T	A	4: 21,873,800 (GRCm39)		probably benign	Het
Ptpn6	T	C	6: 124,702,242 (GRCm39)	H346R	probably benign	Het
Rsf1	T	C	7: 97,311,226 (GRCm39)	V652A	possibly damaging	Het
Rubcn	G	A	16: 32,649,056 (GRCm39)	H624Y	probably damaging	Het
Semp2l2a	T	C	8: 13,887,870 (GRCm39)	R74G	probably benign	Het
Setdb2	T	C	14: 59,644,153 (GRCm39)	N656D	probably benign	Het
Slc22a23	T	C	13: 34,483,076 (GRCm39)	T268A	probably benign	Het
Slc3a1	A	T	17: 85,340,222 (GRCm39)	T215S	possibly damaging	Het
Srsf2	A	G	11: 116,742,904 (GRCm39)	S206P	probably benign	Het
Susd2	T	A	10: 75,475,184 (GRCm39)	D542V	probably damaging	Het
Svep1	G	A	4: 58,073,121 (GRCm39)	Q2063*	probably null	Het
Syne2	G	A	12: 75,977,757 (GRCm39)	V1401M	possibly damaging	Het
Tenm2	A	G	11: 36,834,803 (GRCm39)	L64P	probably damaging	Het
Tigd2	A	G	6: 59,188,272 (GRCm39)	T380A	possibly damaging	Het
Trmt12	G	T	15: 58,745,834 (GRCm39)	V411F	probably damaging	Het
Ubr4	T	C	4: 139,163,613 (GRCm39)		probably null	Het
Ush2a	G	A	1: 188,554,935 (GRCm39)	C3571Y	probably benign	Het
Usp8	A	G	2: 126,562,030 (GRCm39)	M75V	possibly damaging	Het
Vcan	C	T	13: 89,852,825 (GRCm39)	D712N	probably damaging	Het
Vcan	C	A	13: 89,860,386 (GRCm39)	R327L	probably damaging	Het
Vps8	A	G	16: 21,253,683 (GRCm39)	E8G	probably benign	Het
Washc5	T	C	15: 59,231,258 (GRCm39)	D335G	probably benign	Het
Zbtb39	A	G	10: 127,578,704 (GRCm39)	N426S	probably benign	Het
Zfp184	T	A	13: 22,133,919 (GRCm39)	D55E	probably damaging	Het
Zfp882	T	C	8: 72,668,181 (GRCm39)	V336A	probably benign	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
R0195:Phgdh	UTSW	3	98,223,866 (GRCm39)	unclassified	probably benign
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'- TGTGTCCGTGTGCTTAGCATCC -3'
(R):5'- ACTGTTGTAAACTTGGCTCAGGGG -3'

Sequencing Primer
(F):5'- TAATCACTGACCTCGCGGAA -3'
(R):5'- GAACTGGGCCAAACTACTCTTC -3'

Posted On

2013-07-11