Mutagenetix > Incidental Mutation

Incidental Mutation 'R3917:Pnpo'

307372

Institutional Source

Beutler Lab

Gene Symbol

Pnpo

Ensembl Gene

ENSMUSG00000018659

Gene Name

pyridoxine 5'-phosphate oxidase

Synonyms

MMRRC Submission

040914-MU

Accession Numbers

Essential gene?

Possibly non essential (E-score: 0.335) question?

Stock #

R3917 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

96828651-96834812 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 96830583 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Valine to Alanine at position 146 (V146A)

Ref Sequence

ENSEMBL: ENSMUSP00000018803 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000018803] [ENSMUST00000054311] [ENSMUST00000062172] [ENSMUST00000107629] [ENSMUST00000107633] [ENSMUST00000107636]

AlphaFold

Q91XF0

Predicted Effect

probably damaging
Transcript: ENSMUST00000018803
AA Change: V146A

PolyPhen 2 Score 0.997 (Sensitivity: 0.41; Specificity: 0.98)

SMART Domains

Protein: ENSMUSP00000018803
Gene: ENSMUSG00000018659
AA Change: V146A

Domain	Start	End	E-Value	Type
Pfam:Pyridox_oxase_2	59	149	3.9e-8	PFAM
Pfam:Pyridox_oxidase	60	153	2.4e-27	PFAM
Pfam:PNPOx_C	206	261	2.8e-19	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000054311

SMART Domains

Protein: ENSMUSP00000056614
Gene: ENSMUSG00000047040

Domain	Start	End	E-Value	Type
Pfam:ATAD4	6	88	3.7e-33	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000062172

SMART Domains

Protein: ENSMUSP00000056647
Gene: ENSMUSG00000047040

Domain	Start	End	E-Value	Type
Pfam:ATAD4	6	87	1.3e-26	PFAM

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000107628

Predicted Effect

probably benign
Transcript: ENSMUST00000107629

SMART Domains

Protein: ENSMUSP00000103255
Gene: ENSMUSG00000018659

Domain	Start	End	E-Value	Type
PDB:1NRG\|A	1	92	2e-49	PDB
SCOP:d1dnla_	57	86	3e-4	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000107633

SMART Domains

Protein: ENSMUSP00000103259
Gene: ENSMUSG00000047040

Domain	Start	End	E-Value	Type
Pfam:ATAD4	6	88	3.7e-33	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000107636

SMART Domains

Protein: ENSMUSP00000103262
Gene: ENSMUSG00000047040

Domain	Start	End	E-Value	Type
Pfam:ATAD4	6	88	3.7e-33	PFAM

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000131501

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000153896

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000135825

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000186326

Meta Mutation Damage Score

0.3608

Coding Region Coverage

1x: 99.3%
3x: 98.7%
10x: 97.3%
20x: 95.0%

Validation Efficiency

97% (74/76)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The enzyme encoded by this gene catalyzes the terminal, rate-limiting step in the synthesis of pyridoxal 5'-phosphate, also known as vitamin B6. Vitamin B6 is a required co-factor for enzymes involved in both homocysteine metabolism and synthesis of neurotransmitters such as catecholamine. Mutations in this gene result in pyridoxamine 5'-phosphate oxidase (PNPO) deficiency, a form of neonatal epileptic encephalopathy. [provided by RefSeq, Oct 2008]

Allele List at MGI

Other mutations in this stock

Total: 74 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Acad12	A	G	5: 121,737,277 (GRCm39)	V498A	probably damaging	Het
Adam19	A	G	11: 45,951,762 (GRCm39)	E37G	probably benign	Het
Apol11b	A	G	15: 77,519,504 (GRCm39)	I192T	probably benign	Het
Appl1	A	T	14: 26,650,561 (GRCm39)	F537Y	probably damaging	Het
Atad5	A	C	11: 79,994,120 (GRCm39)	K785N	probably null	Het
Atp1b2	A	G	11: 69,493,901 (GRCm39)	V93A	probably damaging	Het
Bcam	T	C	7: 19,499,375 (GRCm39)	Y216C	probably damaging	Het
Brca2	A	G	5: 150,464,292 (GRCm39)	E1352G	probably damaging	Het
C030005K15Rik	A	C	10: 97,561,453 (GRCm39)	S93A	unknown	Het
Cadps	C	T	14: 12,457,702 (GRCm38)	A1060T	probably benign	Het
Ccdc88c	A	G	12: 100,907,366 (GRCm39)		probably null	Het
Ccdc89	A	G	7: 90,076,033 (GRCm39)	D81G	probably damaging	Het
Ccnt1	A	G	15: 98,441,940 (GRCm39)	S443P	probably benign	Het
Cd109	CATTTATTTATTTATTTATTTATTTATTTATTTAT	CATTTATTTATTTATTTATTTATTTATTTATTTATTTAT	9: 78,619,782 (GRCm39)		probably benign	Het
Cdc42bpa	T	C	1: 179,933,719 (GRCm39)		probably null	Het
Cdk11b	T	C	4: 155,711,258 (GRCm39)	S47P	probably damaging	Het
Cfap43	T	C	19: 47,886,189 (GRCm39)	D142G	probably benign	Het
Cntnap4	C	G	8: 113,602,165 (GRCm39)	P1190A	probably benign	Het
Colgalt2	T	A	1: 152,384,362 (GRCm39)	Y567*	probably null	Het
Dner	CGCTGCTGCTGCTGCTGCTGCTGCTGC	CGCTGCTGCTGCTGCTGCTGCTGC	1: 84,563,270 (GRCm39)		probably benign	Het
Dock7	T	C	4: 98,904,922 (GRCm39)	Y651C	probably damaging	Het
Fzd3	A	T	14: 65,473,379 (GRCm39)	F130I	probably damaging	Het
Gabarapl2	T	A	8: 112,679,028 (GRCm39)	F115L	probably benign	Het
Gm1043	G	A	5: 37,350,285 (GRCm39)		probably benign	Het
Gm12185	A	G	11: 48,806,760 (GRCm39)	F144L	probably benign	Het
Gm21961	A	T	15: 64,886,733 (GRCm39)	D7E	unknown	Het
Gtf3a	A	G	5: 146,892,244 (GRCm39)	K332E	probably benign	Het
Haao	A	G	17: 84,146,228 (GRCm39)		probably null	Het
Habp2	T	A	19: 56,299,611 (GRCm39)	C170S	probably damaging	Het
Heatr3	T	G	8: 88,876,999 (GRCm39)		probably null	Het
Herc1	T	G	9: 66,341,748 (GRCm39)	C1846G	possibly damaging	Het
Hivep3	T	C	4: 119,956,624 (GRCm39)	S1647P	probably benign	Het
Hnrnpul1	C	T	7: 25,426,300 (GRCm39)	R517Q	probably damaging	Het
Hspg2	A	G	4: 137,286,625 (GRCm39)	E3648G	probably damaging	Het
Jaml	T	C	9: 45,012,449 (GRCm39)		probably benign	Het
Jund	C	T	8: 71,151,673 (GRCm39)		probably benign	Het
Klra14-ps	T	C	6: 130,134,595 (GRCm39)		noncoding transcript	Het
Krt88	G	A	15: 101,350,809 (GRCm39)		probably null	Het
Lrp5	G	A	19: 3,662,330 (GRCm39)	R173C	probably damaging	Het
Lyzl4	T	A	9: 121,412,101 (GRCm39)	D105V	probably damaging	Het
Mst1	A	G	9: 107,961,494 (GRCm39)	I575V	probably benign	Het
Myd88	T	C	9: 119,170,464 (GRCm39)		probably benign	Het
Myo1d	A	T	11: 80,557,404 (GRCm39)	V512E	probably damaging	Het
Ndufv1	A	G	19: 4,060,002 (GRCm39)	Y33H	probably damaging	Het
Nwd1	T	A	8: 73,394,439 (GRCm39)	C608*	probably null	Het
Or10al2	T	A	17: 37,983,684 (GRCm39)	F257I	probably damaging	Het
Or8b37	A	T	9: 37,958,841 (GRCm39)	I108F	probably damaging	Het
Patj	A	T	4: 98,480,245 (GRCm39)	K1317*	probably null	Het
Pld5	A	G	1: 175,791,504 (GRCm39)	S501P	probably benign	Het
Ppdpf	A	G	2: 180,829,521 (GRCm39)	Y16C	probably benign	Het
Ppp1r27	A	G	11: 120,441,785 (GRCm39)	V32A	possibly damaging	Het
Rbm28	T	C	6: 29,154,788 (GRCm39)	D294G	probably benign	Het
Sdk1	T	A	5: 142,036,999 (GRCm39)	D817E	probably damaging	Het
Shank3	A	G	15: 89,387,587 (GRCm39)	D252G	possibly damaging	Het
Slc29a1	A	T	17: 45,899,899 (GRCm39)		probably null	Het
Slc35a5	G	C	16: 44,978,521 (GRCm39)		probably benign	Het
Slc6a5	T	C	7: 49,561,617 (GRCm39)	S50P	probably damaging	Het
Slfn8	A	T	11: 82,907,819 (GRCm39)	Y241*	probably null	Het
Slu7	G	T	11: 43,331,511 (GRCm39)		probably null	Het
Smad2	T	A	18: 76,421,008 (GRCm39)	D82E	probably benign	Het
Spx	A	C	6: 142,359,757 (GRCm39)	E33A	probably damaging	Het
Tdp1	A	G	12: 99,860,976 (GRCm39)	Y205C	probably damaging	Het
Tekt1	A	G	11: 72,236,574 (GRCm39)	I296T	possibly damaging	Het
Tgm1	G	A	14: 55,950,214 (GRCm39)		probably benign	Het
Tnks	A	G	8: 35,320,515 (GRCm39)	S719P	probably damaging	Het
Trip6	A	G	5: 137,311,941 (GRCm39)	C47R	probably benign	Het
Trpv3	A	G	11: 73,174,560 (GRCm39)	D309G	possibly damaging	Het
Tti2	A	G	8: 31,643,547 (GRCm39)	K221E	possibly damaging	Het
Ugcg	C	T	4: 59,207,798 (GRCm39)	P46S	probably benign	Het
Vmn1r57	A	T	7: 5,223,630 (GRCm39)	N52Y	probably damaging	Het
Vmn2r94	A	G	17: 18,464,620 (GRCm39)	F557L	probably benign	Het
Zbed5	T	C	5: 129,931,118 (GRCm39)	Y356H	possibly damaging	Het
Zfp1005	T	A	2: 150,108,039 (GRCm39)		probably benign	Het
Zic4	C	A	9: 91,266,394 (GRCm39)		probably benign	Het

Other mutations in Pnpo

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00970:Pnpo	APN	11	96,834,618 (GRCm39)	missense	possibly damaging	0.90
IGL01646:Pnpo	APN	11	96,829,775 (GRCm39)	missense	possibly damaging	0.93
IGL01654:Pnpo	APN	11	96,834,555 (GRCm39)	critical splice donor site	probably null
IGL02081:Pnpo	APN	11	96,830,150 (GRCm39)	missense	probably damaging	0.99
IGL03153:Pnpo	APN	11	96,834,661 (GRCm39)	missense	probably damaging	1.00
IGL03179:Pnpo	APN	11	96,830,085 (GRCm39)	missense	possibly damaging	0.79
R0398:Pnpo	UTSW	11	96,833,253 (GRCm39)	nonsense	probably null
R4418:Pnpo	UTSW	11	96,831,795 (GRCm39)	splice site	probably null
R5214:Pnpo	UTSW	11	96,833,295 (GRCm39)	missense	probably benign	0.07
R5427:Pnpo	UTSW	11	96,834,633 (GRCm39)	missense	probably benign	0.02
R9584:Pnpo	UTSW	11	96,831,705 (GRCm39)	nonsense	probably null
X0052:Pnpo	UTSW	11	96,834,634 (GRCm39)	missense	possibly damaging	0.71

Predicted Primers

PCR Primer
(F):5'- GCTAGTTTGACAAGACCCTGG -3'
(R):5'- TGTAGGAATCATGTTCTGCCTG -3'

Sequencing Primer
(F):5'- AGTTTGACAAGACCCTGGCATCTC -3'
(R):5'- ATCATGTTCTGCCTGGGCCTG -3'

Posted On

2015-04-17