Mutagenetix > Incidental Mutation

Incidental Mutation 'R4153:Pgk2'

315018

Institutional Source

Beutler Lab

Gene Symbol

Pgk2

Ensembl Gene

ENSMUSG00000031233

Gene Name

phosphoglycerate kinase 2

Synonyms

Tcp-2, Tcp-2, Pgk-2

MMRRC Submission

040997-MU

Accession Numbers

Essential gene?

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

Stock #

R4153 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

40517909-40519500 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 40519149 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Valine to Alanine at position 93 (V93A)

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 damaging
Transcript: ENSMUST00000033585
AA Change: V93A

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000033585
Gene: ENSMUSG00000031233
AA Change: V93A

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

Meta Mutation Damage Score

0.9148

Coding Region Coverage

1x: 99.2%
3x: 98.6%
10x: 97.4%
20x: 95.7%

Validation Efficiency

96% (53/55)

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: 46 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
2210408I21Rik	T	C	13: 77,341,292 (GRCm39)	V47A	probably benign	Het
4932414N04Rik	A	T	2: 68,498,941 (GRCm39)		probably benign	Het
Acat2	T	A	17: 13,171,153 (GRCm39)	H159L	possibly damaging	Het
Acsl5	A	G	19: 55,269,895 (GRCm39)	E253G	probably benign	Het
Adam34l	T	A	8: 44,079,564 (GRCm39)	Y220F	probably benign	Het
Ddx41	G	A	13: 55,682,293 (GRCm39)	R205W	possibly damaging	Het
Ebf2	T	G	14: 67,472,672 (GRCm39)	V30G	probably damaging	Het
Erlin1	T	A	19: 44,056,056 (GRCm39)	T60S	probably benign	Het
Fanca	A	G	8: 124,031,617 (GRCm39)	V358A	possibly damaging	Het
Fastkd3	T	C	13: 68,738,257 (GRCm39)	F602S	probably damaging	Het
Fras1	C	A	5: 96,924,594 (GRCm39)	N3678K	probably benign	Het
Gopc	T	C	10: 52,225,239 (GRCm39)	I277V	probably damaging	Het
Gpd2	A	G	2: 57,245,783 (GRCm39)	T438A	probably damaging	Het
Gzma	T	C	13: 113,232,802 (GRCm39)	K97E	possibly damaging	Het
Gzmn	T	A	14: 56,405,299 (GRCm39)	T62S	probably damaging	Het
Hip1	T	C	5: 135,441,560 (GRCm39)	E570G	probably damaging	Het
Hs3st6	T	C	17: 24,977,339 (GRCm39)	V273A	possibly damaging	Het
Jarid2	C	A	13: 45,063,902 (GRCm39)	S873R	probably damaging	Het
Klk14	G	A	7: 43,341,501 (GRCm39)	C51Y	probably damaging	Het
Mast2	T	C	4: 116,173,160 (GRCm39)	N548S	possibly damaging	Het
Mthfr	G	T	4: 148,135,932 (GRCm39)	R335L	probably damaging	Het
Ndst3	T	C	3: 123,465,876 (GRCm39)	Y32C	probably damaging	Het
Nwd1	T	C	8: 73,408,564 (GRCm39)	L808P	probably damaging	Het
Or52b1	T	C	7: 104,978,592 (GRCm39)	N269S	probably damaging	Het
Or56a3b	A	T	7: 104,771,516 (GRCm39)	H284L	probably damaging	Het
Or8g52	A	C	9: 39,631,296 (GRCm39)	M258L	probably benign	Het
Pigk	G	A	3: 152,445,766 (GRCm39)	V126I	probably damaging	Het
Plcl2	A	T	17: 50,913,389 (GRCm39)	K133*	probably null	Het
Pofut2	A	G	10: 77,104,500 (GRCm39)	K426E	probably benign	Het
Rbpj	T	A	5: 53,806,789 (GRCm39)	H230Q	probably damaging	Het
Rnf213	A	G	11: 119,300,308 (GRCm39)	K269E	probably benign	Het
Shh	A	T	5: 28,662,947 (GRCm39)	I407N	probably damaging	Het
Sntg1	A	T	1: 8,653,569 (GRCm39)		probably null	Het
Svep1	A	T	4: 58,089,426 (GRCm39)	F1661Y	possibly damaging	Het
Tep1	G	A	14: 51,075,051 (GRCm39)	H1755Y	possibly damaging	Het
Thrap3	A	C	4: 126,067,235 (GRCm39)		probably null	Het
Thumpd1	C	T	7: 119,319,816 (GRCm39)	C50Y	probably damaging	Het
Tmem131	T	C	1: 36,847,874 (GRCm39)		probably benign	Het
Tnrc18	T	C	5: 142,751,747 (GRCm39)	D1368G	possibly damaging	Het
Tubd1	G	A	11: 86,440,296 (GRCm39)	G107S	probably damaging	Het
Ugt1a6a	A	G	1: 88,066,193 (GRCm39)		probably null	Het
Uty	A	G	Y: 1,158,327 (GRCm39)	V572A	possibly damaging	Het
Vmn1r171	A	G	7: 23,332,077 (GRCm39)	K89E	probably damaging	Het
Vmn2r100	AAAACAGGAGTATTGATTGGAAAC	AAAAC	17: 19,743,681 (GRCm39)		probably null	Het
Vmn2r106	A	G	17: 20,488,080 (GRCm39)	L773P	probably damaging	Het
Vps13b	T	A	15: 35,792,173 (GRCm39)		probably null	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
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
R6415:Pgk2	UTSW	17	40,518,459 (GRCm39)	missense	probably benign	0.00
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'- CAGTGATGCTTGGAAGGCTTC -3'
(R):5'- GAGAGTAGACTTCAACGTTCCCATG -3'

Sequencing Primer
(F):5'- CTACTTTAGCAGGGTCAGCAC -3'
(R):5'- TTCAACGTTCCCATGAAGAATAAC -3'

Posted On

2015-05-14