Mutagenetix > Incidental Mutation

Incidental Mutation 'R2495:Phgdh'

250935

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

040409-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R2495 (G1)

Quality Score

123

Status

Validated

Chromosome

Chromosomal Location

98220487-98247285 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 98247105 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Leucine to Proline at position 15 (L15P)

Ref Sequence

ENSEMBL: ENSMUSP00000064755 (fasta)

Gene Model

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

AlphaFold

Q61753

Predicted Effect

probably damaging
Transcript: ENSMUST00000065793
AA Change: L15P

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

SMART Domains

Protein: ENSMUSP00000064755
Gene: ENSMUSG00000053398
AA Change: L15P

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

Meta Mutation Damage Score

0.7135

Coding Region Coverage

1x: 99.2%
3x: 98.6%
10x: 97.3%
20x: 95.2%

Validation Efficiency

98% (63/64)

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: 61 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1810062G17Rik	T	C	3: 36,536,109 (GRCm39)	F125S	unknown	Het
Abhd17c	C	T	7: 83,759,884 (GRCm39)	W290*	probably null	Het
Acsl5	A	T	19: 55,282,031 (GRCm39)	K536*	probably null	Het
Adamts14	A	T	10: 61,034,749 (GRCm39)		probably null	Het
Agbl3	A	G	6: 34,823,699 (GRCm39)	H788R	probably damaging	Het
Agrp	T	C	8: 106,293,408 (GRCm39)	N126D	possibly damaging	Het
Ambn	T	C	5: 88,615,663 (GRCm39)	I349T	probably benign	Het
Ank1	T	C	8: 23,622,280 (GRCm39)	W1610R	probably damaging	Het
Aox3	T	C	1: 58,227,567 (GRCm39)	L1224P	probably damaging	Het
Arhgef28	A	T	13: 98,165,881 (GRCm39)		probably benign	Het
Bcl11b	G	A	12: 107,881,706 (GRCm39)	H798Y	possibly damaging	Het
Capn11	T	A	17: 45,949,689 (GRCm39)	M426L	probably damaging	Het
Cep95	A	G	11: 106,700,108 (GRCm39)	K290E	possibly damaging	Het
Cic	A	G	7: 24,991,201 (GRCm39)		probably benign	Het
Cnbd1	A	T	4: 18,860,579 (GRCm39)	M389K	probably damaging	Het
Cnksr1	A	T	4: 133,959,473 (GRCm39)	L387Q	probably benign	Het
Cntrob	G	T	11: 69,213,749 (GRCm39)	P14T	probably damaging	Het
Crmp1	G	A	5: 37,403,441 (GRCm39)		probably null	Het
Dido1	A	G	2: 180,331,181 (GRCm39)	V89A	probably benign	Het
Dnah7a	T	A	1: 53,645,040 (GRCm39)	I999F	probably damaging	Het
Dsp	T	A	13: 38,377,453 (GRCm39)	L1746Q	possibly damaging	Het
Dst	T	C	1: 34,238,454 (GRCm39)	S3897P	probably damaging	Het
Fbxo10	A	G	4: 45,040,545 (GRCm39)	F887L	probably benign	Het
Gm21961	T	A	15: 64,886,722 (GRCm39)	H11L	unknown	Het
Gm4559	A	T	7: 141,827,557 (GRCm39)	C182S	unknown	Het
Golga3	T	A	5: 110,355,462 (GRCm39)	S939T	probably damaging	Het
Got2	A	G	8: 96,614,918 (GRCm39)	S6P	possibly damaging	Het
Gpatch8	A	T	11: 102,369,307 (GRCm39)	H1410Q	probably damaging	Het
Gpx5	T	A	13: 21,475,610 (GRCm39)	T39S	probably benign	Het
Grin2b	T	C	6: 135,710,180 (GRCm39)	Y1122C	probably damaging	Het
Gsn	A	C	2: 35,193,205 (GRCm39)	N538T	probably damaging	Het
Helz2	A	G	2: 180,874,705 (GRCm39)	S1930P	probably damaging	Het
Krt6b	A	T	15: 101,586,757 (GRCm39)	F286Y	probably damaging	Het
Lrriq1	G	A	10: 103,038,242 (GRCm39)	R854C	probably damaging	Het
Mipol1	A	T	12: 57,507,776 (GRCm39)		probably benign	Het
Mmp19	A	G	10: 128,626,819 (GRCm39)		probably benign	Het
Msc	T	G	1: 14,825,473 (GRCm39)	Y167S	probably benign	Het
Mycbp2	T	G	14: 103,437,554 (GRCm39)	K2103Q	probably damaging	Het
Myh11	C	A	16: 14,023,421 (GRCm39)	D1586Y	probably damaging	Het
Nol6	A	T	4: 41,118,427 (GRCm39)	D791E	probably damaging	Het
Pcm1	A	G	8: 41,746,616 (GRCm39)	T1272A	probably benign	Het
Ptprk	A	T	10: 28,351,074 (GRCm39)		probably benign	Het
Ralgapa2	G	T	2: 146,203,320 (GRCm39)	D1091E	possibly damaging	Het
Rbbp8nl	C	A	2: 179,920,895 (GRCm39)	K496N	probably null	Het
Rbm26	T	C	14: 105,388,748 (GRCm39)		probably benign	Het
Rfx6	A	C	10: 51,602,771 (GRCm39)		probably benign	Het
Rras	G	A	7: 44,667,488 (GRCm39)	G17R	probably damaging	Het
Shisa6	G	A	11: 66,108,459 (GRCm39)	P473S	probably damaging	Het
Slc9a3	A	G	13: 74,306,822 (GRCm39)	K316E	probably damaging	Het
Slco1a7	C	A	6: 141,711,503 (GRCm39)	M69I	probably benign	Het
Spata31d1a	A	G	13: 59,849,807 (GRCm39)	S774P	possibly damaging	Het
Spsb4	T	C	9: 96,877,840 (GRCm39)	Y161C	probably damaging	Het
Taf3	G	T	2: 9,957,644 (GRCm39)	N174K	probably damaging	Het
Tectb	C	G	19: 55,169,431 (GRCm39)		probably benign	Het
Trnt1	T	A	6: 106,750,330 (GRCm39)	V78E	possibly damaging	Het
Ubox5	A	T	2: 130,441,441 (GRCm39)	C415*	probably null	Het
Ucn2	C	T	9: 108,815,477 (GRCm39)	P80S	possibly damaging	Het
Vmn2r10	G	A	5: 109,143,961 (GRCm39)	T663I	probably damaging	Het
Wdfy1	A	T	1: 79,685,222 (GRCm39)	F337L	probably null	Het
Zfp287	A	T	11: 62,605,459 (GRCm39)	C483S	probably damaging	Het
Zyg11b	A	G	4: 108,101,921 (GRCm39)		probably null	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
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'- CCCGGGACCAACTGATAAGATAG -3'
(R):5'- AGCATTTCTGACCAATCAAAAGGAG -3'

Sequencing Primer
(F):5'- CCAACTGATAAGATAGGGGAGGAC -3'
(R):5'- AAGGAGACTGTTGGCGC -3'

Posted On

2014-12-04