Mutagenetix > Incidental Mutation

Incidental Mutation 'R5457:Agps'

432793

Institutional Source

Beutler Lab

Gene Symbol

Agps

Ensembl Gene

ENSMUSG00000042410

Gene Name

alkylglycerone phosphate synthase

Synonyms

9930035G10Rik, bs2, ADAPS

MMRRC Submission

043020-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R5457 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

75662521-75761694 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 75684596 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Tyrosine to Cysteine at position 188 (Y188C)

Ref Sequence

ENSEMBL: ENSMUSP00000107583 (fasta)

Gene Model

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

AlphaFold

no structure available at present

Predicted Effect

probably benign
Transcript: ENSMUST00000047232
AA Change: Y188C

PolyPhen 2 Score 0.004 (Sensitivity: 0.98; Specificity: 0.59)

SMART Domains

Protein: ENSMUSP00000041967
Gene: ENSMUSG00000042410
AA Change: Y188C

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 benign
Transcript: ENSMUST00000111952
AA Change: Y188C

PolyPhen 2 Score 0.007 (Sensitivity: 0.96; Specificity: 0.75)

SMART Domains

Protein: ENSMUSP00000107583
Gene: ENSMUSG00000042410
AA Change: Y188C

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 benign
Transcript: ENSMUST00000175646
AA Change: Y85C

PolyPhen 2 Score 0.004 (Sensitivity: 0.98; Specificity: 0.59)

SMART Domains

Protein: ENSMUSP00000135457
Gene: ENSMUSG00000042410
AA Change: Y85C

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

Coding Region Coverage

1x: 99.2%
3x: 98.5%
10x: 96.9%
20x: 94.3%

Validation Efficiency

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: 64 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abcc12	C	A	8: 87,236,473 (GRCm39)	V1114L	probably benign	Het
Actr5	G	A	2: 158,477,918 (GRCm39)		probably null	Het
Adcy7	T	C	8: 89,037,649 (GRCm39)	L239P	probably damaging	Het
Afg3l1	T	A	8: 124,216,707 (GRCm39)	F315L	possibly damaging	Het
Akt1	T	C	12: 112,623,525 (GRCm39)	T312A	probably damaging	Het
Ang2	T	C	14: 51,433,292 (GRCm39)	Y30C	probably damaging	Het
Angpt1	G	A	15: 42,386,916 (GRCm39)	T146I	probably damaging	Het
Atg16l1	T	C	1: 87,702,813 (GRCm39)	S288P	probably damaging	Het
Atp1b2	C	T	11: 69,493,558 (GRCm39)	G4R	probably damaging	Het
Best3	T	C	10: 116,840,416 (GRCm39)	F282S	probably damaging	Het
Cdkn2b	A	G	4: 89,225,391 (GRCm39)	L98P	probably damaging	Het
Cenps	A	G	4: 149,216,094 (GRCm39)		probably null	Het
Clec16a	G	T	16: 10,363,396 (GRCm39)		probably null	Het
Cxcl13	A	T	5: 96,104,830 (GRCm39)	M1L	unknown	Het
Dcun1d4	A	T	5: 73,688,908 (GRCm39)	E149D	probably damaging	Het
Dlst	G	A	12: 85,168,914 (GRCm39)		probably null	Het
Dock10	C	A	1: 80,501,781 (GRCm39)	C1803F	probably damaging	Het
Dpp10	T	A	1: 123,339,539 (GRCm39)	K329N	possibly damaging	Het
Drosha	T	G	15: 12,926,115 (GRCm39)	Y1235D	probably benign	Het
Eif2s3y	G	A	Y: 1,016,057 (GRCm39)	G213D	probably damaging	Homo
Eps8	A	T	6: 137,489,175 (GRCm39)	S408T	probably damaging	Het
Fam171a2	T	C	11: 102,328,362 (GRCm39)	D799G	possibly damaging	Het
Fcho2	T	C	13: 98,926,275 (GRCm39)	K103E	probably damaging	Het
Fcrlb	T	C	1: 170,739,726 (GRCm39)	T59A	probably damaging	Het
Fgd4	T	C	16: 16,279,873 (GRCm39)	R395G	probably benign	Het
Gm14496	A	T	2: 181,639,401 (GRCm39)	D497V	probably damaging	Het
Gpt2	A	C	8: 86,238,967 (GRCm39)	N267H	possibly damaging	Het
Grb14	A	T	2: 64,747,442 (GRCm39)	C43S	probably damaging	Het
Hjurp	T	TN	1: 88,194,247 (GRCm39)		probably null	Het
Igkv8-16	A	G	6: 70,363,689 (GRCm39)	V111A	possibly damaging	Het
Klra2	T	A	6: 131,198,852 (GRCm39)	S230C	possibly damaging	Het
Lamb3	G	A	1: 193,008,302 (GRCm39)	R245H	probably damaging	Het
Lamc3	A	G	2: 31,821,997 (GRCm39)	E1315G	probably benign	Het
Lpin2	A	G	17: 71,550,367 (GRCm39)	T672A	probably damaging	Het
Mcoln3	T	A	3: 145,833,877 (GRCm39)	I139N	probably benign	Het
Mcpt8	C	T	14: 56,319,793 (GRCm39)	C219Y	probably benign	Het
Mtcl3	A	C	10: 29,072,720 (GRCm39)	I671L	probably benign	Het
Mug2	G	T	6: 122,026,688 (GRCm39)	G541*	probably null	Het
Myo7b	G	T	18: 32,104,503 (GRCm39)		probably null	Het
Or10j2	C	T	1: 173,098,141 (GRCm39)	S133L	probably benign	Het
Or10j7	A	G	1: 173,011,180 (GRCm39)	S274P	probably damaging	Het
Or5ac22	T	C	16: 59,135,213 (GRCm39)	I186V	probably benign	Het
Or5k8	A	T	16: 58,644,796 (GRCm39)	I92N	probably damaging	Het
Or7e176	A	T	9: 20,171,574 (GRCm39)	Y146F	probably damaging	Het
Pclo	C	T	5: 14,726,157 (GRCm39)		probably benign	Het
Pdk2	C	T	11: 94,919,408 (GRCm39)	S289N	probably damaging	Het
Pex19	G	T	1: 171,958,245 (GRCm39)	G75W	probably damaging	Het
Psma3	T	G	12: 71,031,339 (GRCm39)	S26A	probably benign	Het
Pth1r	A	T	9: 110,555,522 (GRCm39)	I326N	possibly damaging	Het
Sbf2	T	C	7: 109,912,037 (GRCm39)	T1670A	probably benign	Het
Scn10a	A	G	9: 119,523,193 (GRCm39)	Y67H	probably damaging	Het
Sec16a	A	T	2: 26,330,280 (GRCm39)	D578E	probably benign	Het
Spta1	C	T	1: 174,044,759 (GRCm39)	A1465V	probably damaging	Het
Taar9	A	G	10: 23,985,003 (GRCm39)	F144L	probably damaging	Het
Tal1	T	C	4: 114,925,777 (GRCm39)	V282A	probably benign	Het
Tbrg4	C	T	11: 6,570,947 (GRCm39)	R175Q	probably damaging	Het
Tdp1	C	T	12: 99,861,005 (GRCm39)	Q215*	probably null	Het
Thsd4	A	T	9: 59,887,060 (GRCm39)	W921R	probably damaging	Het
Trrap	A	G	5: 144,786,787 (GRCm39)	E3462G	probably damaging	Het
Try4	T	C	6: 41,280,355 (GRCm39)	S60P	probably damaging	Het
Ttn	T	C	2: 76,541,265 (GRCm39)	E25580G	probably damaging	Het
Ttn	A	T	2: 76,776,299 (GRCm39)	I1581N	possibly damaging	Het
Vmn2r50	T	C	7: 9,781,873 (GRCm39)	T291A	probably damaging	Het
Zkscan14	T	C	5: 145,138,169 (GRCm39)	D106G	probably benign	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
R5418:Agps	UTSW	2	75,689,248 (GRCm39)	missense	probably damaging	1.00
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'- TTACCAAGTTGGACTCTAGTACTTG -3'
(R):5'- GCCCAGTATGAGTGAGCAAC -3'

Sequencing Primer
(F):5'- ATCATTCTCCTAGCAGAGGG -3'
(R):5'- TGAGCAACACTAGCATGAGC -3'

Posted On

2016-10-06