Mutagenetix > Incidental Mutation

Incidental Mutation 'R0114:Phykpl'

20668

Institutional Source

Beutler Lab

Gene Symbol

Phykpl

Ensembl Gene

ENSMUSG00000020359

Gene Name

5-phosphohydroxy-L-lysine phospholyase

Synonyms

Agxt2l2, 2900006B13Rik

MMRRC Submission

038400-MU

Accession Numbers

Essential gene?

Possibly essential (E-score: 0.569) question?

Stock #

R0114 (G1)

Quality Score

Status

Validated (trace)

Chromosome

Chromosomal Location

51474751-51494091 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

G to A at 51477480 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Aspartic acid to Asparagine at position 91 (D91N)

Ref Sequence

ENSEMBL: ENSMUSP00000132190 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000020625] [ENSMUST00000101250] [ENSMUST00000102765] [ENSMUST00000167797]

AlphaFold

Q8R1K4

Predicted Effect

probably benign
Transcript: ENSMUST00000020625
AA Change: D91N

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

SMART Domains

Protein: ENSMUSP00000020625
Gene: ENSMUSG00000020359
AA Change: D91N

Domain	Start	End	E-Value	Type
low complexity region	14	25	N/A	INTRINSIC
Pfam:Aminotran_3	27	433	2.1e-81	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000101250
AA Change: D91N

PolyPhen 2 Score 0.002 (Sensitivity: 0.99; Specificity: 0.30)

SMART Domains

Protein: ENSMUSP00000098808
Gene: ENSMUSG00000020359
AA Change: D91N

Domain	Start	End	E-Value	Type
low complexity region	14	25	N/A	INTRINSIC
Pfam:Aminotran_3	33	212	8.2e-29	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000102765

SMART Domains

Protein: ENSMUSP00000099826
Gene: ENSMUSG00000063564

Domain	Start	End	E-Value	Type
low complexity region	2	50	N/A	INTRINSIC
Pfam:Collagen	107	162	3.7e-10	PFAM
Pfam:Collagen	140	207	1.3e-9	PFAM
low complexity region	212	237	N/A	INTRINSIC
Pfam:Collagen	239	299	1.8e-11	PFAM
Pfam:Collagen	309	367	1.8e-10	PFAM
Pfam:Collagen	331	390	6.6e-11	PFAM
Pfam:Collagen	402	463	2.4e-11	PFAM
Pfam:Collagen	455	523	3.7e-11	PFAM

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000109105

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000156128

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000164864

Predicted Effect

probably benign
Transcript: ENSMUST00000167797
AA Change: D91N

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

SMART Domains

Protein: ENSMUSP00000132190
Gene: ENSMUSG00000020359
AA Change: D91N

Domain	Start	End	E-Value	Type
low complexity region	14	25	N/A	INTRINSIC
Pfam:Aminotran_3	33	373	1.5e-75	PFAM

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000169823

Meta Mutation Damage Score

0.0922

Coding Region Coverage

1x: 98.6%
3x: 97.4%
10x: 93.2%
20x: 79.2%

Validation Efficiency

100% (99/99)

MGI Phenotype

FUNCTION: This gene overlaps in a tail-to-tail orientation the gene encoding heterogeneous nuclear ribonucleoprotein A/B. The terminal exon of this gene is interspersed with exons of heterogeneous nuclear ribonucleoprotein A/B. [provided by RefSeq, Jul 2008]

Allele List at MGI

Other mutations in this stock

Total: 83 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
2310057J18Rik	T	C	10: 28,861,978 (GRCm39)		probably benign	Het
4933427D14Rik	T	C	11: 72,086,625 (GRCm39)	Y262C	probably damaging	Het
Adamts1	C	A	16: 85,596,502 (GRCm39)	V379L	probably benign	Het
Akt3	T	C	1: 176,894,817 (GRCm39)	D260G	probably damaging	Het
Alms1	T	C	6: 85,596,785 (GRCm39)	L537P	probably benign	Het
Anln	A	T	9: 22,264,642 (GRCm39)	I876N	probably damaging	Het
Ano9	A	T	7: 140,683,152 (GRCm39)		probably benign	Het
Arhgef10l	T	C	4: 140,311,194 (GRCm39)	E218G	probably benign	Het
Arnt2	G	A	7: 83,996,738 (GRCm39)	R63C	probably damaging	Het
Atp9a	G	T	2: 168,552,776 (GRCm39)	Y63*	probably null	Het
Bmpr2	G	T	1: 59,854,499 (GRCm39)	C116F	probably damaging	Het
Cand1	T	C	10: 119,052,427 (GRCm39)	D233G	probably benign	Het
Cftr	A	T	6: 18,282,447 (GRCm39)	H1049L	probably damaging	Het
Ckap5	A	T	2: 91,450,457 (GRCm39)	D1975V	possibly damaging	Het
Cyp26c1	T	C	19: 37,675,081 (GRCm39)	V134A	probably benign	Het
Dnai1	T	C	4: 41,605,686 (GRCm39)		probably benign	Het
Dpp10	T	C	1: 123,413,821 (GRCm39)	I163V	probably benign	Het
Fam151a	A	T	4: 106,591,201 (GRCm39)	I15F	possibly damaging	Het
Fanca	A	T	8: 124,015,230 (GRCm39)		probably null	Het
Fes	A	G	7: 80,027,783 (GRCm39)	V787A	probably damaging	Het
Fnip1	C	T	11: 54,378,627 (GRCm39)		probably benign	Het
Gabpb1	A	G	2: 126,495,494 (GRCm39)	I86T	probably damaging	Het
Gmds	A	T	13: 32,411,264 (GRCm39)	S57T	probably benign	Het
Gnpat	T	G	8: 125,610,096 (GRCm39)	D426E	probably benign	Het
Gnptab	C	A	10: 88,269,262 (GRCm39)	P655Q	possibly damaging	Het
Gpi-ps	A	G	8: 5,690,359 (GRCm39)		noncoding transcript	Het
Herc1	T	A	9: 66,369,128 (GRCm39)	F2941I	probably damaging	Het
Herc2	T	C	7: 55,803,522 (GRCm39)		probably benign	Het
Ino80	G	A	2: 119,213,441 (GRCm39)	R1249C	probably damaging	Het
Itga11	T	G	9: 62,642,575 (GRCm39)	V166G	probably damaging	Het
Itga11	T	C	9: 62,667,584 (GRCm39)	V639A	possibly damaging	Het
Itpr2	A	G	6: 146,214,377 (GRCm39)	F1490S	probably damaging	Het
Lama2	C	A	10: 26,869,064 (GRCm39)	E802*	probably null	Het
Lgi3	C	T	14: 70,768,469 (GRCm39)		probably benign	Het
Limch1	C	T	5: 67,193,427 (GRCm39)		probably benign	Het
Lipc	T	C	9: 70,711,063 (GRCm39)	N363S	probably damaging	Het
Lrit2	A	G	14: 36,790,002 (GRCm39)		probably null	Het
Mfsd13a	C	T	19: 46,354,943 (GRCm39)	T40I	probably benign	Het
Mug2	A	G	6: 122,017,607 (GRCm39)	Y448C	probably damaging	Het
Mybpc3	A	G	2: 90,954,839 (GRCm39)	E450G	probably damaging	Het
Myo5b	A	T	18: 74,875,242 (GRCm39)	T1549S	probably benign	Het
Naa15	T	C	3: 51,355,859 (GRCm39)		probably null	Het
Nckap1l	T	A	15: 103,363,455 (GRCm39)	C54S	probably benign	Het
Nlrp9b	A	G	7: 19,757,981 (GRCm39)	D406G	probably benign	Het
Nprl3	T	A	11: 32,189,784 (GRCm39)		probably benign	Het
Nvl	A	G	1: 180,947,956 (GRCm39)	V429A	probably benign	Het
Opa1	A	T	16: 29,448,453 (GRCm39)	N912Y	probably benign	Het
Or14j3	A	T	17: 37,900,306 (GRCm39)	*313K	probably null	Het
Or1x2	G	A	11: 50,918,431 (GRCm39)	V201I	probably benign	Het
Or52b4i	A	T	7: 102,191,938 (GRCm39)	Q265L	probably benign	Het
Or6c211	T	A	10: 129,505,467 (GRCm39)	Y307F	probably benign	Het
Pcnx1	T	C	12: 82,042,869 (GRCm39)	V2317A	possibly damaging	Het
Phf3	A	T	1: 30,844,524 (GRCm39)	N1478K	possibly damaging	Het
Polr2b	T	A	5: 77,491,110 (GRCm39)	C984S	probably damaging	Het
Ppfibp1	A	G	6: 146,899,731 (GRCm39)	R141G	probably benign	Het
Ppm1d	G	A	11: 85,217,731 (GRCm39)	G20R	probably damaging	Het
Ppp1r16a	C	T	15: 76,574,999 (GRCm39)		probably benign	Het
Ppp2r5b	C	A	19: 6,278,461 (GRCm39)	V483F	probably benign	Het
Ppp4r4	T	A	12: 103,542,633 (GRCm39)	C132S	probably benign	Het
Prg2	A	G	2: 84,813,800 (GRCm39)		probably benign	Het
Prpf4b	G	A	13: 35,074,471 (GRCm39)		probably benign	Het
Rad54l2	T	C	9: 106,590,654 (GRCm39)	T491A	probably damaging	Het
Rnf213	G	T	11: 119,305,413 (GRCm39)	W548L	probably damaging	Het
Rusc2	G	T	4: 43,422,055 (GRCm39)	C825F	probably damaging	Het
Sema4b	A	G	7: 79,868,826 (GRCm39)		probably benign	Het
Sema6a	A	G	18: 47,423,244 (GRCm39)	V254A	probably damaging	Het
Slc13a3	A	G	2: 165,266,501 (GRCm39)	F346L	probably damaging	Het
Slc25a17	T	C	15: 81,222,160 (GRCm39)	D104G	probably damaging	Het
Specc1	A	T	11: 62,037,139 (GRCm39)	N707Y	possibly damaging	Het
Tex48	T	A	4: 63,526,696 (GRCm39)	E76V	probably damaging	Het
Tfr2	T	C	5: 137,575,727 (GRCm39)	V281A	probably benign	Het
Tgfb1i1	A	C	7: 127,848,666 (GRCm39)	Q238H	probably damaging	Het
Thoc6	G	A	17: 23,889,213 (GRCm39)	T122I	probably benign	Het
Tmtc1	G	A	6: 148,314,328 (GRCm39)		probably benign	Het
Tnfrsf8	T	C	4: 145,014,617 (GRCm39)	D264G	possibly damaging	Het
Trim43a	T	A	9: 88,466,213 (GRCm39)	I178N	probably damaging	Het
Ttn	G	C	2: 76,537,437 (GRCm39)	I26503M	possibly damaging	Het
Usp28	C	A	9: 48,950,323 (GRCm39)	D589E	probably benign	Het
Utp23	T	C	15: 51,745,907 (GRCm39)	S242P	probably damaging	Het
Vwa3a	A	G	7: 120,374,603 (GRCm39)	Y305C	probably benign	Het
Vwa5b1	C	A	4: 138,336,169 (GRCm39)	E142*	probably null	Het
Xrn2	A	T	2: 146,871,699 (GRCm39)	T374S	probably damaging	Het
Zfp735	A	T	11: 73,601,488 (GRCm39)	Q144L	probably benign	Het

Other mutations in Phykpl

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01336:Phykpl	APN	11	51,490,283 (GRCm39)	splice site	probably benign
IGL01809:Phykpl	APN	11	51,490,351 (GRCm39)	missense	probably benign	0.09
IGL02636:Phykpl	APN	11	51,489,540 (GRCm39)	missense	probably damaging	1.00
IGL02668:Phykpl	APN	11	51,484,514 (GRCm39)	critical splice donor site	probably null
R0308:Phykpl	UTSW	11	51,484,423 (GRCm39)	splice site	probably benign
R0332:Phykpl	UTSW	11	51,477,502 (GRCm39)	missense	probably benign	0.30
R0831:Phykpl	UTSW	11	51,476,366 (GRCm39)	nonsense	probably null
R3434:Phykpl	UTSW	11	51,489,482 (GRCm39)	missense	probably benign
R4272:Phykpl	UTSW	11	51,476,355 (GRCm39)	missense	probably damaging	1.00
R4539:Phykpl	UTSW	11	51,484,915 (GRCm39)	missense	probably damaging	1.00
R4618:Phykpl	UTSW	11	51,483,056 (GRCm39)	missense	probably damaging	1.00
R4633:Phykpl	UTSW	11	51,484,435 (GRCm39)	missense	probably damaging	1.00
R4816:Phykpl	UTSW	11	51,483,780 (GRCm39)	missense	probably benign
R4823:Phykpl	UTSW	11	51,477,420 (GRCm39)	missense	probably damaging	0.99
R5415:Phykpl	UTSW	11	51,476,342 (GRCm39)	missense	probably benign	0.00
R5920:Phykpl	UTSW	11	51,493,622 (GRCm39)	missense	probably benign
R6370:Phykpl	UTSW	11	51,477,543 (GRCm39)	missense	probably damaging	1.00
R6611:Phykpl	UTSW	11	51,489,181 (GRCm39)	missense	probably damaging	1.00
R6617:Phykpl	UTSW	11	51,484,781 (GRCm39)	missense	probably damaging	1.00
R7319:Phykpl	UTSW	11	51,489,530 (GRCm39)	missense	probably benign	0.20
R7340:Phykpl	UTSW	11	51,490,370 (GRCm39)	missense	probably damaging	1.00
R7499:Phykpl	UTSW	11	51,482,285 (GRCm39)	missense	probably damaging	1.00
R7947:Phykpl	UTSW	11	51,477,408 (GRCm39)	missense	probably damaging	0.98
R8146:Phykpl	UTSW	11	51,476,408 (GRCm39)	missense	probably damaging	1.00
R8353:Phykpl	UTSW	11	51,489,121 (GRCm39)	missense	probably damaging	1.00
R8453:Phykpl	UTSW	11	51,489,121 (GRCm39)	missense	probably damaging	1.00
R9101:Phykpl	UTSW	11	51,483,741 (GRCm39)	missense	probably benign	0.05
R9157:Phykpl	UTSW	11	51,490,375 (GRCm39)	missense	probably benign	0.10
R9295:Phykpl	UTSW	11	51,482,231 (GRCm39)	missense	possibly damaging	0.77
R9794:Phykpl	UTSW	11	51,489,212 (GRCm39)	missense	probably benign

Predicted Primers

PCR Primer
(F):5'- CTTGCTTTGACCATGTTGGCACG -3'
(R):5'- GGATCTACAACCTAGAAGCCCAGGAG -3'

Sequencing Primer
(F):5'- AGCTCTAAGAATGCAGATGCC -3'
(R):5'- AGCCTCGCCATGAAGTTG -3'

Posted On

2013-04-11