Mutagenetix > Incidental Mutation

Incidental Mutation 'R5062:Phgdh'

386667

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

042652-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R5062 (G1)

Quality Score

152

Status

Validated

Chromosome

Chromosomal Location

98220487-98247285 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 98235655 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Isoleucine to Phenylalanine at position 121 (I121F)

Ref Sequence

ENSEMBL: ENSMUSP00000064755 (fasta)

Gene Model

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

AlphaFold

Q61753

Predicted Effect

probably damaging
Transcript: ENSMUST00000065793
AA Change: I121F

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

SMART Domains

Protein: ENSMUSP00000064755
Gene: ENSMUSG00000053398
AA Change: I121F

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: I92F

SMART Domains

Protein: ENSMUSP00000117525
Gene: ENSMUSG00000053398
AA Change: I92F

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

0.8279

Coding Region Coverage

1x: 99.0%
3x: 98.2%
10x: 95.7%
20x: 90.1%

Validation Efficiency

100% (79/79)

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: 68 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abca6	A	T	11: 110,067,892 (GRCm39)	I1593N	probably benign	Het
Akr1b10	G	T	6: 34,369,041 (GRCm39)	K173N	probably damaging	Het
Artn	A	T	4: 117,784,873 (GRCm39)	L3Q	probably damaging	Het
Asxl3	T	A	18: 22,655,775 (GRCm39)	S1262T	possibly damaging	Het
Atp6v0a4	A	T	6: 38,051,118 (GRCm39)	M420K	probably benign	Het
Bcam	T	A	7: 19,494,026 (GRCm39)	T422S	possibly damaging	Het
Casp2	C	T	6: 42,246,206 (GRCm39)		probably benign	Het
Ccdc137	A	G	11: 120,353,341 (GRCm39)		probably benign	Het
Cd177	C	A	7: 24,443,741 (GRCm39)	A786S	probably benign	Het
Cdca4	T	C	12: 112,785,483 (GRCm39)	N82D	probably benign	Het
Clu	A	C	14: 66,217,177 (GRCm39)	T337P	probably damaging	Het
Col6a3	A	C	1: 90,707,074 (GRCm39)	I2013S	unknown	Het
Cpne9	T	A	6: 113,281,449 (GRCm39)	M510K	probably damaging	Het
Cyp3a13	A	C	5: 137,897,161 (GRCm39)	N384K	possibly damaging	Het
Fam186a	A	C	15: 99,842,527 (GRCm39)	I1239S	possibly damaging	Het
Fryl	T	C	5: 73,233,236 (GRCm39)	E413G	possibly damaging	Het
Fscn2	A	C	11: 120,257,575 (GRCm39)	Y312S	probably damaging	Het
Fshr	A	T	17: 89,293,474 (GRCm39)	C401*	probably null	Het
Glyat	A	C	19: 12,627,627 (GRCm39)	Q74P	probably damaging	Het
Gm6158	A	T	14: 24,120,158 (GRCm39)		noncoding transcript	Het
Grm7	A	G	6: 110,623,097 (GRCm39)	N90S	probably damaging	Het
Hectd1	A	T	12: 51,791,662 (GRCm39)	C2536S	probably damaging	Het
Herc3	C	T	6: 58,832,745 (GRCm39)	Q137*	probably null	Het
Kctd3	A	C	1: 188,727,890 (GRCm39)		probably benign	Het
Klhl30	A	G	1: 91,283,300 (GRCm39)	T301A	probably benign	Het
Klra9	T	C	6: 130,156,072 (GRCm39)	K228E	possibly damaging	Het
Lamc3	A	T	2: 31,795,679 (GRCm39)	T355S	possibly damaging	Het
Lcmt1	A	C	7: 123,010,053 (GRCm39)		probably null	Het
Limch1	C	T	5: 67,126,578 (GRCm39)	P60S	probably damaging	Het
Lrfn2	A	G	17: 49,377,528 (GRCm39)	D203G	probably damaging	Het
Mc5r	T	C	18: 68,472,352 (GRCm39)	L237P	probably damaging	Het
Mknk2	G	A	10: 80,507,603 (GRCm39)	R58W	probably damaging	Het
Mrgpra2b	T	C	7: 47,152,676 (GRCm39)		probably benign	Het
Mroh2a	GCCC	GC	1: 88,159,979 (GRCm39)		probably null	Het
Nae1	A	T	8: 105,243,334 (GRCm39)	C395S	possibly damaging	Het
Ncoa1	A	G	12: 4,309,333 (GRCm39)	M1321T	probably damaging	Het
Neb	A	C	2: 52,170,513 (GRCm39)	F1720V	possibly damaging	Het
Nectin2	C	T	7: 19,472,198 (GRCm39)	V64I	probably benign	Het
Nisch	T	A	14: 30,894,397 (GRCm39)	T1145S	probably damaging	Het
Nlrp5	A	T	7: 23,135,335 (GRCm39)	R1009*	probably null	Het
Or12d13	A	T	17: 37,647,822 (GRCm39)	H100Q	probably damaging	Het
Or4k15	T	A	14: 50,364,894 (GRCm39)	Y287N	probably damaging	Het
Otx1	C	A	11: 21,947,037 (GRCm39)	A91S	probably damaging	Het
Pak1ip1	A	G	13: 41,161,621 (GRCm39)		probably benign	Het
Pcm1	T	C	8: 41,712,297 (GRCm39)	V189A	probably damaging	Het
Peak1	G	T	9: 56,167,573 (GRCm39)	N118K	probably damaging	Het
Pi4ka	G	T	16: 17,127,261 (GRCm39)	A1064E	probably benign	Het
Pkhd1	A	C	1: 20,655,935 (GRCm39)	C199W	probably benign	Het
Plat	A	G	8: 23,262,327 (GRCm39)	D117G	probably benign	Het
Ppp2r2b	C	A	18: 42,821,526 (GRCm39)	V211L	possibly damaging	Het
Ptgs1	A	G	2: 36,127,294 (GRCm39)	D60G	probably damaging	Het
Ryr2	T	C	13: 11,715,240 (GRCm39)	E2776G	probably damaging	Het
Sema4c	C	T	1: 36,592,059 (GRCm39)		probably null	Het
Sharpin	T	C	15: 76,231,811 (GRCm39)		probably benign	Het
Slamf6	A	G	1: 171,764,100 (GRCm39)	I164M	possibly damaging	Het
Slco1a7	A	C	6: 141,713,180 (GRCm39)	M67R	possibly damaging	Het
Spef1	A	G	2: 131,015,201 (GRCm39)	Y46H	probably damaging	Het
Spns1	G	A	7: 125,973,501 (GRCm39)		probably benign	Het
Supt5	C	T	7: 28,028,440 (GRCm39)		probably null	Het
Tbx5	T	A	5: 119,974,987 (GRCm39)	D3E	probably damaging	Het
Thbs1	T	C	2: 117,951,718 (GRCm39)		probably null	Het
Tmem140	G	A	6: 34,849,897 (GRCm39)	V138M	probably damaging	Het
Tmem200a	T	A	10: 25,869,813 (GRCm39)	D152V	probably damaging	Het
Tmem200b	A	G	4: 131,649,848 (GRCm39)	D256G	probably damaging	Het
Tns1	A	T	1: 73,992,023 (GRCm39)	L885Q	probably damaging	Het
Umod	G	A	7: 119,071,644 (GRCm39)	Q366*	probably null	Het
Vsir	A	G	10: 60,200,042 (GRCm39)	I208V	probably damaging	Het
Zfp646	G	A	7: 127,479,671 (GRCm39)	R616H	probably 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
R0195:Phgdh	UTSW	3	98,223,866 (GRCm39)	unclassified	probably benign
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
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'- TGAACTGCAACCAGAAAGGC -3'
(R):5'- CCCAAGTCATGTCCTACCAATG -3'

Sequencing Primer
(F):5'- CAAAAGGCAAAGATGACCAAGTC -3'
(R):5'- AAGTCATGTCCTACCAATGTTCTCAC -3'

Posted On

2016-06-06