Mutagenetix > Incidental Mutation

Incidental Mutation 'R5378:Phgdh'

425677

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

042953-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R5378 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

98220487-98247285 bp(-) (GRCm39)

Type of Mutation

splice site (2 bp from exon)

DNA Base Change (assembly)

A to T at 98228639 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Gene Model

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

AlphaFold

Q61753

Predicted Effect

possibly damaging
Transcript: ENSMUST00000065793
AA Change: I178N

PolyPhen 2 Score 0.758 (Sensitivity: 0.85; Specificity: 0.92)

SMART Domains

Protein: ENSMUSP00000064755
Gene: ENSMUSG00000053398
AA Change: I178N

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 null
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: 99.3%
3x: 98.7%
10x: 97.5%
20x: 96.0%

Validation Efficiency

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: 60 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abat	T	A	16: 8,396,141 (GRCm39)	F39L	probably benign	Het
Abca2	T	G	2: 25,336,080 (GRCm39)	L2150R	probably damaging	Het
Apob	T	A	12: 8,061,865 (GRCm39)	V3449D	probably damaging	Het
Arfgef2	T	A	2: 166,715,548 (GRCm39)	V1331D	probably damaging	Het
Bora	A	G	14: 99,305,929 (GRCm39)	N433D	probably damaging	Het
Cand2	G	A	6: 115,778,912 (GRCm39)	A1159T	probably benign	Het
Ccser1	C	T	6: 61,288,650 (GRCm39)	A271V	probably benign	Het
Ccser2	G	A	14: 36,601,391 (GRCm39)	T331I	possibly damaging	Het
Cemip	A	G	7: 83,607,733 (GRCm39)	S758P	probably damaging	Het
Cenpf	C	T	1: 189,385,663 (GRCm39)	V2206I	possibly damaging	Het
Chrnb1	A	T	11: 69,676,007 (GRCm39)	S412T	probably benign	Het
Cks1b	A	C	3: 89,323,608 (GRCm39)	W54G	probably damaging	Het
Col5a3	C	T	9: 20,708,872 (GRCm39)	V630M	unknown	Het
Dnajb14	A	G	3: 137,591,139 (GRCm39)	D30G	probably benign	Het
Dpp8	T	C	9: 64,985,296 (GRCm39)	Y785H	probably damaging	Het
Dsel	T	A	1: 111,790,551 (GRCm39)		probably benign	Het
Dzip1	C	T	14: 119,148,805 (GRCm39)	M291I	probably damaging	Het
Esp8	G	A	17: 40,841,033 (GRCm39)	C98Y	unknown	Het
F11	C	A	8: 45,705,180 (GRCm39)	M120I	probably benign	Het
Fsip2	T	C	2: 82,820,185 (GRCm39)	F5306S	possibly damaging	Het
Gm4841	T	C	18: 60,404,113 (GRCm39)		probably null	Het
Gpr180	T	A	14: 118,377,251 (GRCm39)	L84Q	probably benign	Het
Grwd1	A	T	7: 45,479,505 (GRCm39)	D123E	probably benign	Het
Hsfy2	T	C	1: 56,675,827 (GRCm39)	R237G	probably benign	Het
Htr5a	A	G	5: 28,055,993 (GRCm39)	Y328C	probably damaging	Het
Klrb1f	G	A	6: 129,030,794 (GRCm39)	A127T	probably damaging	Het
Mcpt4	A	T	14: 56,299,750 (GRCm39)		probably null	Het
Muc5b	T	C	7: 141,415,940 (GRCm39)	V2962A	unknown	Het
Or52s19	T	A	7: 103,007,652 (GRCm39)	I250F	probably damaging	Het
Or5t15	A	T	2: 86,681,807 (GRCm39)	N78K	probably benign	Het
Otog	A	T	7: 45,904,428 (GRCm39)	T518S	probably damaging	Het
Pip5kl1	A	T	2: 32,469,106 (GRCm39)	T213S	probably benign	Het
Plekhg2	G	A	7: 28,062,094 (GRCm39)	R594W	probably damaging	Het
Prg4	T	A	1: 150,330,977 (GRCm39)		probably benign	Het
Prpf40a	T	A	2: 53,035,888 (GRCm39)	D621V	probably damaging	Het
Ptgr3	G	A	18: 84,112,803 (GRCm39)	A160T	probably damaging	Het
Ptprz1	A	T	6: 23,007,401 (GRCm39)	I1655F	probably damaging	Het
Rbm28	T	C	6: 29,128,558 (GRCm39)	K55E	probably damaging	Het
Rbm43	A	T	2: 51,815,633 (GRCm39)	V196E	probably damaging	Het
Rufy4	T	C	1: 74,186,822 (GRCm39)	C537R	probably damaging	Het
Serinc4	T	A	2: 121,282,861 (GRCm39)	M434L	possibly damaging	Het
Slc22a30	G	A	19: 8,321,757 (GRCm39)	Q436*	probably null	Het
Slc35f1	A	T	10: 52,567,157 (GRCm39)	H22L	possibly damaging	Het
Smg6	A	G	11: 74,932,820 (GRCm39)	D98G	possibly damaging	Het
Strbp	A	G	2: 37,489,186 (GRCm39)	Y527H	probably damaging	Het
Strbp	A	G	2: 37,490,818 (GRCm39)	V479A	probably benign	Het
Tdg	G	T	10: 82,477,305 (GRCm39)	V119L	probably benign	Het
Trav10d	G	A	14: 53,048,825 (GRCm39)	R72H	probably benign	Het
Trgc2	T	C	13: 19,489,297 (GRCm39)	Y145C	unknown	Het
Trim25	T	C	11: 88,900,093 (GRCm39)	L280P	probably damaging	Het
Tsc22d4	A	G	5: 137,760,726 (GRCm39)	D49G	probably damaging	Het
Ttn	T	C	2: 76,720,534 (GRCm39)		probably benign	Het
Tyr	T	A	7: 87,121,703 (GRCm39)	H363L	probably damaging	Het
Ubr5	A	G	15: 37,989,822 (GRCm39)	S2020P	probably damaging	Het
Usp9y	T	C	Y: 1,315,928 (GRCm39)	D2069G	probably damaging	Het
Vmn1r170	T	C	7: 23,305,963 (GRCm39)	W122R	probably benign	Het
Wdr7	G	A	18: 63,958,310 (GRCm39)		probably null	Het
Ylpm1	T	A	12: 85,077,029 (GRCm39)	H793Q	probably damaging	Het
Zfp266	G	A	9: 20,410,659 (GRCm39)	T506I	probably damaging	Het
Zfp518a	T	C	19: 40,904,300 (GRCm39)	S1410P	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
R5062:Phgdh	UTSW	3	98,235,655 (GRCm39)	missense	probably damaging	1.00
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'- AAGTATCATCATGCTCAGCAGG -3'
(R):5'- TGTCTCAGGGCTTCCAAGAC -3'

Sequencing Primer
(F):5'- ATGCTCAGCAGGCCCCAG -3'
(R):5'- ACACCGAAGTTGCTCCTG -3'

Posted On

2016-08-04