Mutagenetix > Incidental Mutation

Incidental Mutation 'R5418:Agps'

427829

Institutional Source

Beutler Lab

Gene Symbol

Agps

Ensembl Gene

ENSMUSG00000042410

Gene Name

alkylglycerone phosphate synthase

Synonyms

9930035G10Rik, bs2, ADAPS

MMRRC Submission

042986-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R5418 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

75662521-75761694 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 75689248 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Threonine to Alanine at position 252 (T252A)

Ref Sequence

ENSEMBL: ENSMUSP00000107583 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000047232] [ENSMUST00000111952] [ENSMUST00000175646]

AlphaFold

no structure available at present

Predicted Effect

possibly damaging
Transcript: ENSMUST00000047232
AA Change: T252A

PolyPhen 2 Score 0.879 (Sensitivity: 0.82; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000041967
Gene: ENSMUSG00000042410
AA Change: T252A

Domain	Start	End	E-Value	Type
low complexity region	24	37	N/A	INTRINSIC
low complexity region	73	95	N/A	INTRINSIC
Pfam:FAD_binding_4	219	362	3.2e-43	PFAM
Pfam:FAD-oxidase_C	397	670	4.2e-61	PFAM

Predicted Effect

probably damaging
Transcript: ENSMUST00000111952
AA Change: T252A

PolyPhen 2 Score 0.996 (Sensitivity: 0.55; Specificity: 0.98)

SMART Domains

Protein: ENSMUSP00000107583
Gene: ENSMUSG00000042410
AA Change: T252A

Domain	Start	End	E-Value	Type
low complexity region	24	37	N/A	INTRINSIC
low complexity region	73	95	N/A	INTRINSIC
Pfam:FAD_binding_4	219	362	4.7e-43	PFAM
Pfam:FAD-oxidase_C	397	508	5.2e-19	PFAM

Predicted Effect

probably damaging
Transcript: ENSMUST00000175646
AA Change: T149A

PolyPhen 2 Score 0.989 (Sensitivity: 0.72; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000135457
Gene: ENSMUSG00000042410
AA Change: T149A

Domain	Start	End	E-Value	Type
Pfam:FAD_binding_4	116	259	1.2e-43	PFAM
Pfam:FAD-oxidase_C	294	567	2.6e-61	PFAM

Meta Mutation Damage Score

0.9024

Coding Region Coverage

1x: 99.3%
3x: 98.6%
10x: 97.3%
20x: 95.4%

Validation Efficiency

99% (81/82)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene is a member of the FAD-binding oxidoreductase/transferase type 4 family. It encodes a protein that catalyzes the second step of ether lipid biosynthesis in which acyl-dihydroxyacetonephosphate (DHAP) is converted to alkyl-DHAP by the addition of a long chain alcohol and the removal of a long-chain acid anion. The protein is localized to the inner aspect of the peroxisomal membrane and requires FAD as a cofactor. Mutations in this gene have been associated with rhizomelic chondrodysplasia punctata, type 3 and Zellweger syndrome. [provided by RefSeq, Jul 2008]
PHENOTYPE: Mice homozygous for a spontaneous allele exhibit male infertility, azoospermia, microphthalmia, and cataracts. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 75 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4930568D16Rik	A	G	2: 35,244,738 (GRCm39)	S205P	probably damaging	Het
Abcc1	T	C	16: 14,278,996 (GRCm39)	V1102A	probably benign	Het
Acad8	A	T	9: 26,896,853 (GRCm39)	M202K	probably damaging	Het
Acoxl	T	A	2: 127,719,722 (GRCm39)	M161K	probably benign	Het
Adamts4	T	A	1: 171,080,143 (GRCm39)	V35E	probably damaging	Het
Add2	A	G	6: 86,087,894 (GRCm39)	S614G	probably benign	Het
Adgrv1	T	A	13: 81,567,427 (GRCm39)	I5249L	probably benign	Het
Alms1-ps1	G	A	6: 85,732,584 (GRCm39)		noncoding transcript	Het
Ankrd24	T	A	10: 81,480,776 (GRCm39)		probably benign	Het
Bcl9l	A	G	9: 44,416,733 (GRCm39)	Q218R	possibly damaging	Het
Bin2	T	C	15: 100,547,027 (GRCm39)	Y232C	probably damaging	Het
Bptf	A	G	11: 107,002,120 (GRCm39)	Y331H	probably damaging	Het
Ccr10	C	T	11: 101,064,904 (GRCm39)	V209M	probably benign	Het
Cflar	A	T	1: 58,791,810 (GRCm39)	D371V	possibly damaging	Het
Col1a2	A	G	6: 4,516,931 (GRCm39)		probably benign	Het
Crlf2	A	G	5: 109,704,899 (GRCm39)	V104A	probably benign	Het
Dennd1c	CCGCCCCTCGCTGACAGC	CC	17: 57,373,755 (GRCm39)		probably null	Het
Dmxl2	A	G	9: 54,281,935 (GRCm39)		probably null	Het
Dnah17	C	A	11: 117,985,810 (GRCm39)	E1422D	probably benign	Het
Dnase1l1	C	T	X: 73,320,644 (GRCm39)		probably null	Het
Efcab11	A	G	12: 99,821,877 (GRCm39)	L80S	possibly damaging	Het
Emc8	G	A	8: 121,385,342 (GRCm39)	T130M	probably damaging	Het
Epha6	C	A	16: 60,245,198 (GRCm39)	A334S	possibly damaging	Het
Erc2	A	G	14: 27,688,467 (GRCm39)	M196V	probably benign	Het
Etnk2	T	C	1: 133,300,995 (GRCm39)	I254T	probably damaging	Het
Fam120b	C	T	17: 15,622,061 (GRCm39)	T13M	probably damaging	Het
Fam234b	A	G	6: 135,203,966 (GRCm39)	K423E	probably benign	Het
Fcgbp	G	A	7: 27,784,738 (GRCm39)	G266D	probably damaging	Het
Fndc4	A	T	5: 31,451,978 (GRCm39)	S146R	probably benign	Het
Frmd3	G	A	4: 74,079,935 (GRCm39)		probably null	Het
Glrx2	C	A	1: 143,615,446 (GRCm39)	S16R	possibly damaging	Het
Gm26526	T	G	7: 39,238,358 (GRCm39)		noncoding transcript	Het
Hc	C	T	2: 34,898,195 (GRCm39)		probably null	Het
Herc2	T	C	7: 55,787,313 (GRCm39)	C1695R	probably damaging	Het
Hic1	A	G	11: 75,057,425 (GRCm39)		probably null	Het
Igkv4-92	A	T	6: 68,732,564 (GRCm39)	V5E	possibly damaging	Het
Irs1	G	A	1: 82,266,491 (GRCm39)	T575I	probably damaging	Het
Kcp	A	T	6: 29,504,283 (GRCm39)	Y143*	probably null	Het
Klb	A	G	5: 65,540,813 (GRCm39)	N969D	probably benign	Het
Klra6	T	A	6: 129,990,393 (GRCm39)	L239F	probably damaging	Het
Lhx6	A	G	2: 35,977,378 (GRCm39)		probably null	Het
Lrrc34	G	A	3: 30,696,923 (GRCm39)	P116S	possibly damaging	Het
Map3k9	T	A	12: 81,790,591 (GRCm39)	K321*	probably null	Het
Mapk14	T	C	17: 28,960,817 (GRCm39)	V196A	possibly damaging	Het
Matcap2	G	T	9: 22,343,066 (GRCm39)	R187L	probably damaging	Het
Mmp1b	T	C	9: 7,384,897 (GRCm39)	I251V	possibly damaging	Het
Mtmr12	T	C	15: 12,270,045 (GRCm39)	L711P	probably damaging	Het
Mylk	T	C	16: 34,732,600 (GRCm39)	S627P	probably benign	Het
Nbea	A	T	3: 55,553,410 (GRCm39)	Y2631N	possibly damaging	Het
Ncoa7	A	G	10: 30,524,035 (GRCm39)	V153A	probably damaging	Het
Or4a79	T	C	2: 89,552,343 (GRCm39)	I37M	probably benign	Het
Pax6	A	T	2: 105,521,910 (GRCm39)	D175V	probably benign	Het
Piezo1	A	G	8: 123,213,519 (GRCm39)	L1793P	probably damaging	Het
Pkp4	T	C	2: 59,140,506 (GRCm39)	V404A	probably benign	Het
Plxnb2	A	G	15: 89,050,694 (GRCm39)	Y421H	probably benign	Het
Prkdc	T	G	16: 15,612,961 (GRCm39)	V3173G	probably benign	Het
Prss40	A	T	1: 34,599,840 (GRCm39)	I49N	probably benign	Het
Prx	T	A	7: 27,216,699 (GRCm39)	V400E	probably damaging	Het
Rbm11	A	C	16: 75,393,423 (GRCm39)	T40P	probably damaging	Het
Resf1	T	C	6: 149,227,634 (GRCm39)	Y227H	probably damaging	Het
Scara5	CG	C	14: 65,997,111 (GRCm39)		probably null	Het
Sema3f	A	G	9: 107,569,820 (GRCm39)	Y70H	probably damaging	Het
Senp6	G	A	9: 80,029,151 (GRCm39)	E505K	possibly damaging	Het
Slc25a3	T	C	10: 90,955,398 (GRCm39)	I147M	probably benign	Het
Slc4a7	T	A	14: 14,760,280 (GRCm38)	S572T	probably benign	Het
Smarcal1	C	T	1: 72,638,068 (GRCm39)	P501S	probably benign	Het
Sox7	C	T	14: 64,185,396 (GRCm39)	T144M	probably benign	Het
Taar1	T	C	10: 23,797,214 (GRCm39)	F304S	possibly damaging	Het
Tcf3	A	G	10: 80,263,517 (GRCm39)	F46L	probably damaging	Het
Tmem184c	A	G	8: 78,324,449 (GRCm39)	V347A	probably damaging	Het
Tpcn2	C	T	7: 144,832,518 (GRCm39)	E113K	probably damaging	Het
Vmn1r232	T	A	17: 21,134,378 (GRCm39)	Y74F	possibly damaging	Het
Vmn2r102	C	T	17: 19,914,415 (GRCm39)	T660I	probably damaging	Het
Zdhhc3	A	G	9: 122,909,456 (GRCm39)	M234T	probably damaging	Het
Zfp960	T	A	17: 17,307,805 (GRCm39)	L173H	probably damaging	Het

Other mutations in Agps

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00811:Agps	APN	2	75,756,316 (GRCm39)	missense	probably benign	0.00
IGL01373:Agps	APN	2	75,683,128 (GRCm39)	missense	probably benign	0.00
IGL01958:Agps	APN	2	75,740,045 (GRCm39)	critical splice donor site	probably null
IGL02691:Agps	APN	2	75,722,204 (GRCm39)	missense	probably benign	0.04
R0087:Agps	UTSW	2	75,739,979 (GRCm39)	missense	probably damaging	1.00
R0323:Agps	UTSW	2	75,724,505 (GRCm39)	nonsense	probably null
R1116:Agps	UTSW	2	75,692,269 (GRCm39)	splice site	probably benign
R1511:Agps	UTSW	2	75,697,123 (GRCm39)	missense	probably damaging	1.00
R2049:Agps	UTSW	2	75,689,270 (GRCm39)	missense	probably benign
R4770:Agps	UTSW	2	75,722,199 (GRCm39)	missense	possibly damaging	0.94
R5457:Agps	UTSW	2	75,684,596 (GRCm39)	missense	probably benign	0.01
R6795:Agps	UTSW	2	75,724,402 (GRCm39)	missense	probably damaging	0.98
R7286:Agps	UTSW	2	75,683,128 (GRCm39)	missense	probably benign	0.22
R7367:Agps	UTSW	2	75,698,657 (GRCm39)	missense	possibly damaging	0.67
R7529:Agps	UTSW	2	75,662,696 (GRCm39)	missense	possibly damaging	0.85
R7842:Agps	UTSW	2	75,681,876 (GRCm39)	missense	probably damaging	1.00
R8416:Agps	UTSW	2	75,684,547 (GRCm39)	missense	probably benign
R9149:Agps	UTSW	2	75,697,182 (GRCm39)	missense	probably damaging	0.99
R9261:Agps	UTSW	2	75,684,850 (GRCm39)	intron	probably benign
R9371:Agps	UTSW	2	75,742,024 (GRCm39)	critical splice donor site	probably null
R9393:Agps	UTSW	2	75,735,256 (GRCm39)	missense	possibly damaging	0.67
R9453:Agps	UTSW	2	75,662,585 (GRCm39)	missense	probably damaging	0.99
R9555:Agps	UTSW	2	75,683,091 (GRCm39)	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- GCCCATTGAGTTCAGTTCCATAG -3'
(R):5'- TAAAGCACCAAGATCTGTGCC -3'

Sequencing Primer
(F):5'- AGTTCAGTTCCATAGTAGTCTGC -3'
(R):5'- CCAAGATCTGTGCCTTAGAACTTAGC -3'

Posted On

2016-09-01