Mutagenetix > Incidental Mutation

Incidental Mutation 'R6415:Pgk2'

517903

Institutional Source

Beutler Lab

Gene Symbol

Pgk2

Ensembl Gene

ENSMUSG00000031233

Gene Name

phosphoglycerate kinase 2

Synonyms

Tcp-2, Tcp-2, Pgk-2

MMRRC Submission

044557-MU

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.152) question?

Stock #

R6415 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

40517909-40519500 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to T at 40518459 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Isoleucine to Asparagine at position 323 (I323N)

Ref Sequence

ENSEMBL: ENSMUSP00000033585 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000033585]

AlphaFold

P09041

PDB Structure

Crystal Structure of Phosphoglycerate Kinase-2 [X-RAY DIFFRACTION]
Crystal Structure of Phosphoglycerate Kinase-2 bound to 3-phosphoglycerate [X-RAY DIFFRACTION]
Crystal structure of phosphoglycerate kinase-2 bound to atp and 3pg [X-RAY DIFFRACTION]

Predicted Effect

probably benign
Transcript: ENSMUST00000033585
AA Change: I323N

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)

SMART Domains

Protein: ENSMUSP00000033585
Gene: ENSMUSG00000031233
AA Change: I323N

Domain	Start	End	E-Value	Type
Pfam:PGK	9	406	1.3e-152	PFAM

Meta Mutation Damage Score

0.0898

Coding Region Coverage

1x: 99.9%
3x: 99.6%
10x: 97.8%
20x: 93.1%

Validation Efficiency

100% (65/65)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene is intronless, arose via retrotransposition of the phosphoglycerate kinase 1 gene, and is expressed specifically in the testis. Initially assumed to be a pseudogene, the encoded protein is actually a functional phosphoglycerate kinase that catalyzes the reversible conversion of 1,3-bisphosphoglycerate to 3-phosphoglycerate, during the Embden-Meyerhof-Parnas pathway of glycolysis, in the later stages of spermatogenesis.[provided by RefSeq, May 2010]
PHENOTYPE: Mice homozygous for a knock-out allele exhibit decreased male fertility associated with reduced sperm motility. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 66 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4930563M21Rik	G	A	9: 55,881,296 (GRCm39)	T482M	probably benign	Het
Adam9	A	G	8: 25,468,498 (GRCm39)	Y513H	probably damaging	Het
Adamts20	C	T	15: 94,222,540 (GRCm39)		probably null	Het
B3gnt5	A	G	16: 19,588,759 (GRCm39)	D326G	probably damaging	Het
Cacna1g	A	G	11: 94,354,243 (GRCm39)	I224T	probably damaging	Het
Ccdc18	A	G	5: 108,309,612 (GRCm39)	I402M	probably benign	Het
Cckar	A	T	5: 53,860,398 (GRCm39)	C73S	probably damaging	Het
Cdk13	C	T	13: 17,913,739 (GRCm39)	R880H	probably damaging	Het
Col1a1	A	G	11: 94,830,986 (GRCm39)	N218D	unknown	Het
Csnk1g2	T	C	10: 80,474,130 (GRCm39)	I145T	possibly damaging	Het
Cul5	T	C	9: 53,557,983 (GRCm39)	D207G	probably benign	Het
Cyp2c69	A	G	19: 39,831,365 (GRCm39)	F483L	probably benign	Het
Ddx60	A	G	8: 62,436,939 (GRCm39)	D963G	probably benign	Het
Dhx8	G	T	11: 101,628,513 (GRCm39)	A142S	unknown	Het
Dock7	C	T	4: 98,880,685 (GRCm39)	R926Q	probably damaging	Het
Dscaml1	C	T	9: 45,594,975 (GRCm39)	Q693*	probably null	Het
Dysf	G	A	6: 84,117,024 (GRCm39)	C1234Y	probably damaging	Het
Ercc1	G	A	7: 19,089,102 (GRCm39)		probably null	Het
Fam91a1	T	C	15: 58,314,766 (GRCm39)	L549P	probably damaging	Het
Fxyd2	T	A	9: 45,314,592 (GRCm39)	Y5N	possibly damaging	Het
Gab1	C	A	8: 81,515,226 (GRCm39)	R364L	possibly damaging	Het
Gpr182	T	A	10: 127,586,375 (GRCm39)	D192V	possibly damaging	Het
Gps1	T	C	11: 120,678,548 (GRCm39)	V286A	possibly damaging	Het
Grk1	A	G	8: 13,463,127 (GRCm39)	Y383C	probably damaging	Het
H2bc15	T	C	13: 21,938,656 (GRCm39)	Y122H	probably benign	Het
Hic1	G	A	11: 75,057,143 (GRCm39)	P582L	possibly damaging	Het
Igkv4-61	C	A	6: 69,394,138 (GRCm39)	A31S	possibly damaging	Het
Khdc4	T	C	3: 88,607,279 (GRCm39)	F328L	probably benign	Het
Lactb	T	C	9: 66,877,927 (GRCm39)	K301E	possibly damaging	Het
Lrp3	A	T	7: 34,903,593 (GRCm39)	V251E	probably benign	Het
Mapt	G	A	11: 104,189,824 (GRCm39)	G265S	probably benign	Het
Obscn	A	T	11: 58,925,956 (GRCm39)	D6245E	probably damaging	Het
Or10al2	G	T	17: 37,983,448 (GRCm39)	C178F	possibly damaging	Het
Or1j12	A	G	2: 36,342,617 (GRCm39)	S7G	probably damaging	Het
Or4b1c	T	A	2: 90,126,381 (GRCm39)	I275F	probably damaging	Het
Or4c10b	T	C	2: 89,711,206 (GRCm39)	L12P	probably damaging	Het
Or6c207	T	C	10: 129,104,890 (GRCm39)	T101A	probably benign	Het
Or7e165	T	A	9: 19,695,044 (GRCm39)	I205N	probably damaging	Het
Or7g19	T	C	9: 18,856,415 (GRCm39)	L157P	probably damaging	Het
Oxsm	A	T	14: 16,241,904 (GRCm38)	H288Q	probably benign	Het
Pcdh9	C	T	14: 93,253,278 (GRCm39)	M1128I	possibly damaging	Het
Pcdha8	T	C	18: 37,127,614 (GRCm39)	Y699H	probably damaging	Het
Plin4	A	G	17: 56,410,264 (GRCm39)	V1216A	probably damaging	Het
Ppargc1a	T	C	5: 51,620,176 (GRCm39)		probably benign	Het
Prelp	A	T	1: 133,840,516 (GRCm39)	I322N	probably benign	Het
Prelp	A	T	1: 133,842,395 (GRCm39)	I250N	probably damaging	Het
Prss27	T	A	17: 24,261,882 (GRCm39)	C63*	probably null	Het
Rab38	G	A	7: 88,079,748 (GRCm39)	A47T	possibly damaging	Het
Rprd2	G	A	3: 95,681,531 (GRCm39)	A436V	probably benign	Het
Sacs	A	T	14: 61,442,808 (GRCm39)	N1618I	probably damaging	Het
Scp2	T	G	4: 107,962,337 (GRCm39)	S63R	probably benign	Het
Sftpb	T	G	6: 72,281,633 (GRCm39)	W9G	probably damaging	Het
Slco1a4	A	T	6: 141,780,415 (GRCm39)	L125*	probably null	Het
Sptlc1	T	C	13: 53,505,728 (GRCm39)		probably null	Het
Sub1	T	A	15: 11,986,560 (GRCm39)	M96L	probably benign	Het
Tanc1	T	C	2: 59,667,458 (GRCm39)	V1233A	probably benign	Het
Tmem140	A	T	6: 34,849,658 (GRCm39)	D58V	probably damaging	Het
Tmem231	G	A	8: 112,653,524 (GRCm39)		probably benign	Het
Tpt1	T	C	14: 76,083,811 (GRCm39)	Y91H	probably benign	Het
Trap1	C	T	16: 3,861,856 (GRCm39)	R636H	possibly damaging	Het
Ttc14	A	G	3: 33,857,724 (GRCm39)	H275R	possibly damaging	Het
Tut7	T	A	13: 59,964,110 (GRCm39)		probably null	Het
Vps35l	T	C	7: 118,391,869 (GRCm39)	W494R	probably damaging	Het
Ypel1	A	G	16: 16,921,438 (GRCm39)		probably null	Het
Zbtb44	T	A	9: 30,975,510 (GRCm39)	I380N	possibly damaging	Het
Zswim5	T	C	4: 116,838,063 (GRCm39)	F798L	possibly damaging	Het

Other mutations in Pgk2

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
R0195:Pgk2	UTSW	17	40,518,622 (GRCm39)	missense	probably benign	0.01
R1297:Pgk2	UTSW	17	40,519,255 (GRCm39)	missense	probably benign	0.04
R1351:Pgk2	UTSW	17	40,518,691 (GRCm39)	missense	probably damaging	1.00
R1781:Pgk2	UTSW	17	40,519,398 (GRCm39)	missense	probably benign	0.20
R2126:Pgk2	UTSW	17	40,518,400 (GRCm39)	missense	probably damaging	1.00
R3153:Pgk2	UTSW	17	40,519,134 (GRCm39)	missense	probably damaging	0.99
R3154:Pgk2	UTSW	17	40,519,134 (GRCm39)	missense	probably damaging	0.99
R4152:Pgk2	UTSW	17	40,519,149 (GRCm39)	missense	probably damaging	1.00
R4153:Pgk2	UTSW	17	40,519,149 (GRCm39)	missense	probably damaging	1.00
R4154:Pgk2	UTSW	17	40,519,149 (GRCm39)	missense	probably damaging	1.00
R4259:Pgk2	UTSW	17	40,518,274 (GRCm39)	missense	probably benign	0.01
R4261:Pgk2	UTSW	17	40,518,274 (GRCm39)	missense	probably benign	0.01
R4812:Pgk2	UTSW	17	40,518,281 (GRCm39)	missense	possibly damaging	0.56
R4961:Pgk2	UTSW	17	40,518,412 (GRCm39)	missense	probably damaging	1.00
R4989:Pgk2	UTSW	17	40,518,402 (GRCm39)	missense	probably damaging	1.00
R5661:Pgk2	UTSW	17	40,518,287 (GRCm39)	nonsense	probably null
R6246:Pgk2	UTSW	17	40,518,315 (GRCm39)	missense	probably damaging	1.00
R7054:Pgk2	UTSW	17	40,519,366 (GRCm39)	missense	probably benign	0.08
R7721:Pgk2	UTSW	17	40,518,409 (GRCm39)	missense	probably benign	0.12
R8785:Pgk2	UTSW	17	40,518,777 (GRCm39)	missense	probably damaging	1.00
R9014:Pgk2	UTSW	17	40,518,687 (GRCm39)	missense	probably benign
R9057:Pgk2	UTSW	17	40,518,735 (GRCm39)	missense	possibly damaging	0.93
R9253:Pgk2	UTSW	17	40,519,233 (GRCm39)	missense	probably damaging	1.00
R9330:Pgk2	UTSW	17	40,519,078 (GRCm39)	missense	probably benign	0.31
R9654:Pgk2	UTSW	17	40,518,651 (GRCm39)	missense	probably damaging	0.99

Predicted Primers

PCR Primer
(F):5'- GCTGACCTTGTCTTCAGTGC -3'
(R):5'- TGTTTGATGAAGAGGGAGCCAC -3'

Sequencing Primer
(F):5'- GTCTTCAGTGCCCCATTTGG -3'
(R):5'- GCCACGATTGTTAAAGAGATCATG -3'

Posted On

2018-05-24