Mutagenetix > Incidental Mutation

Incidental Mutation 'IGL02991:Pdxdc1'

452946

Institutional Source

Beutler Lab

Gene Symbol

Pdxdc1

Ensembl Gene

ENSMUSG00000022680

Gene Name

pyridoxal-dependent decarboxylase domain containing 1

Synonyms

2210010A19Rik

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.173) question?

Stock #

IGL02991 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

13651012-13720995 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 13675260 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Isoleucine to Threonine at position 334 (I334T)

Ref Sequence

ENSEMBL: ENSMUSP00000111469 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000023361] [ENSMUST00000115802] [ENSMUST00000115803] [ENSMUST00000115804]

AlphaFold

no structure available at present

Predicted Effect

possibly damaging
Transcript: ENSMUST00000023361
AA Change: I357T

PolyPhen 2 Score 0.774 (Sensitivity: 0.85; Specificity: 0.92)

SMART Domains

Protein: ENSMUSP00000023361
Gene: ENSMUSG00000022680
AA Change: I357T

Domain	Start	End	E-Value	Type
Pfam:Pyridoxal_deC	166	310	2.6e-12	PFAM
coiled coil region	610	631	N/A	INTRINSIC
low complexity region	683	695	N/A	INTRINSIC

Predicted Effect

possibly damaging
Transcript: ENSMUST00000115802
AA Change: I357T

PolyPhen 2 Score 0.517 (Sensitivity: 0.88; Specificity: 0.90)

SMART Domains

Protein: ENSMUSP00000111468
Gene: ENSMUSG00000022680
AA Change: I357T

Domain	Start	End	E-Value	Type
Pfam:Pyridoxal_deC	153	316	1.8e-15	PFAM

Predicted Effect

probably damaging
Transcript: ENSMUST00000115803
AA Change: I334T

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

SMART Domains

Protein: ENSMUSP00000111469
Gene: ENSMUSG00000022680
AA Change: I334T

Domain	Start	End	E-Value	Type
Pfam:Pyridoxal_deC	190	293	1.4e-13	PFAM

Predicted Effect

possibly damaging
Transcript: ENSMUST00000115804
AA Change: I357T

PolyPhen 2 Score 0.649 (Sensitivity: 0.87; Specificity: 0.91)

SMART Domains

Protein: ENSMUSP00000111471
Gene: ENSMUSG00000022680
AA Change: I357T

Domain	Start	End	E-Value	Type
Pfam:Pyridoxal_deC	154	308	5.5e-15	PFAM
coiled coil region	610	631	N/A	INTRINSIC
low complexity region	683	695	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000139859

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000154150

Meta Mutation Damage Score

0.8926

Coding Region Coverage

1x: 0.0%
3x: 0.0%
10x: 0.0%
20x: 0.0%

Validation Efficiency

95% (73/77)

Allele List at MGI

Other mutations in this stock

Total: 64 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4933416I08Rik	TCC	TCCC	X: 52,692,862 (GRCm39)		noncoding transcript	Het
Adam23	T	C	1: 63,586,978 (GRCm39)		probably null	Het
Aptx	C	A	4: 40,686,687 (GRCm39)	G199C	probably damaging	Het
Asap2	T	C	12: 21,299,294 (GRCm39)		probably benign	Het
Atp11b	A	G	3: 35,881,140 (GRCm39)	T566A	probably benign	Het
Bcas3	C	T	11: 85,348,713 (GRCm39)	Q202*	probably null	Het
Cacna1h	C	A	17: 25,610,286 (GRCm39)	R740L	possibly damaging	Het
Casp8	T	A	1: 58,866,438 (GRCm39)	N146K	probably benign	Het
Ccdc63	T	C	5: 122,246,275 (GRCm39)	M549V	probably benign	Het
Cdc45	C	T	16: 18,617,479 (GRCm39)	M200I	probably benign	Het
Cdh20	T	C	1: 104,861,972 (GRCm39)	S51P	probably benign	Het
Chd7	T	C	4: 8,828,398 (GRCm39)	M1113T	possibly damaging	Het
Cilp	TGGG	TGG	9: 65,187,412 (GRCm39)		probably null	Het
Crb1	ACC	AC	1: 139,164,822 (GRCm39)		probably null	Het
Crb1	CG	C	1: 139,164,824 (GRCm39)		probably null	Het
Cxcl11	C	T	5: 92,509,169 (GRCm39)	R28H	probably damaging	Het
Defb40	C	T	8: 19,025,119 (GRCm39)	C29Y	probably damaging	Het
Fcna	G	C	2: 25,520,693 (GRCm39)		probably benign	Het
Fen1	A	T	19: 10,178,026 (GRCm39)	D139E	probably benign	Het
Frem3	A	G	8: 81,395,511 (GRCm39)	E1846G	probably damaging	Het
Gria2	T	A	3: 80,615,116 (GRCm39)	K455*	probably null	Het
Hmcn1	A	T	1: 150,614,409 (GRCm39)	N1332K	possibly damaging	Het
Htr5b	C	T	1: 121,455,756 (GRCm39)	V55M	probably benign	Het
Ighv6-5	A	T	12: 114,380,315 (GRCm39)	N86K	probably benign	Het
Il4ra	T	C	7: 125,174,833 (GRCm39)	V347A	possibly damaging	Het
Itih5	A	G	2: 10,256,162 (GRCm39)	E876G	probably benign	Het
Itpkb	A	T	1: 180,155,279 (GRCm39)		probably benign	Het
Lbr	T	C	1: 181,649,117 (GRCm39)	Y334C	probably damaging	Het
Lrfn2	T	C	17: 49,377,732 (GRCm39)	L271P	probably damaging	Het
Lss	T	A	10: 76,379,745 (GRCm39)		probably benign	Het
Map1a	T	C	2: 121,132,091 (GRCm39)	V731A	probably damaging	Het
Mmp1a	TG	TGG	9: 7,465,083 (GRCm38)		probably null	Het
Mob3b	T	A	4: 35,083,805 (GRCm39)	Q128L	probably benign	Het
Mog	T	C	17: 37,334,091 (GRCm39)	M1V	probably null	Het
Mrpl4	A	G	9: 20,919,901 (GRCm39)	Y284C	probably damaging	Het
Mtus2	T	G	5: 148,250,310 (GRCm39)	V310G	probably damaging	Het
Mup11	ACAGCAGCAGCAGCAGCA	ACAGCAGCAGCAGCA	4: 60,618,275 (GRCm39)		probably benign	Het
Odad4	A	G	11: 100,444,698 (GRCm39)	S285G	probably benign	Het
Or10g9	T	C	9: 39,911,698 (GRCm39)	Y275C	probably damaging	Het
Or8g55	T	A	9: 39,785,362 (GRCm39)	S264T	probably benign	Het
Orc3	T	G	4: 34,593,083 (GRCm39)	Q328P	probably damaging	Het
Otulinl	T	C	15: 27,658,388 (GRCm39)	S211G	possibly damaging	Het
Pcdhb20	G	T	18: 37,639,264 (GRCm39)	G597C	probably damaging	Het
Ppef2	C	T	5: 92,383,759 (GRCm39)	W450*	probably null	Het
Proz	G	A	8: 13,123,490 (GRCm39)	E254K	probably benign	Het
Psma6	T	C	12: 55,454,357 (GRCm39)		probably benign	Het
Rbm12	C	T	2: 155,937,480 (GRCm39)		probably benign	Het
Ryr2	A	G	13: 11,776,192 (GRCm39)	V1115A	probably damaging	Het
Sfxn5	G	T	6: 85,266,190 (GRCm39)	N102K	possibly damaging	Het
Sgo2a	G	T	1: 58,054,514 (GRCm39)		probably benign	Het
Slc14a2	A	T	18: 78,249,049 (GRCm39)	M1K	probably null	Het
Spag5	T	A	11: 78,205,077 (GRCm39)	L621M	probably damaging	Het
Spata31	A	G	13: 65,068,533 (GRCm39)	Y227C	probably benign	Het
Speer4c1	A	C	5: 15,919,214 (GRCm39)		probably benign	Het
Supt6	T	C	11: 78,116,179 (GRCm39)	E728G	probably damaging	Het
Sympk	T	A	7: 18,764,502 (GRCm39)	L69Q	probably damaging	Het
Timd4	T	A	11: 46,732,974 (GRCm39)		probably benign	Het
Trh	G	A	6: 92,220,719 (GRCm39)	R48W	probably damaging	Het
Trip12	C	A	1: 84,716,536 (GRCm39)	D383Y	probably damaging	Het
Tspo2	T	A	17: 48,757,014 (GRCm39)	I23F	possibly damaging	Het
Tspyl5	A	G	15: 33,686,989 (GRCm39)	S319P	probably damaging	Het
Txlnb	A	G	10: 17,717,201 (GRCm39)	K403E	probably damaging	Het
Vmn2r34	C	A	7: 7,675,720 (GRCm39)	C556F	probably damaging	Het
Vps13c	C	A	9: 67,821,159 (GRCm39)	A1223E	probably damaging	Het

Other mutations in Pdxdc1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01760:Pdxdc1	APN	16	13,677,016 (GRCm39)	missense	probably damaging	1.00
IGL02101:Pdxdc1	APN	16	13,687,720 (GRCm39)	missense	probably damaging	0.99
IGL02484:Pdxdc1	APN	16	13,693,945 (GRCm39)	missense	possibly damaging	0.94
IGL02523:Pdxdc1	APN	16	13,699,799 (GRCm39)	missense	probably damaging	1.00
IGL02560:Pdxdc1	APN	16	13,657,596 (GRCm39)	missense	probably benign	0.00
IGL02884:Pdxdc1	APN	16	13,661,659 (GRCm39)	missense	possibly damaging	0.86
IGL03008:Pdxdc1	APN	16	13,694,023 (GRCm39)	missense	possibly damaging	0.81
IGL03162:Pdxdc1	APN	16	13,675,281 (GRCm39)	missense	probably damaging	0.99
PIT4472001:Pdxdc1	UTSW	16	13,663,209 (GRCm39)	missense	probably damaging	1.00
R0015:Pdxdc1	UTSW	16	13,705,547 (GRCm39)	splice site	probably benign
R0240:Pdxdc1	UTSW	16	13,697,309 (GRCm39)	missense	probably damaging	1.00
R0240:Pdxdc1	UTSW	16	13,697,309 (GRCm39)	missense	probably damaging	1.00
R0432:Pdxdc1	UTSW	16	13,672,264 (GRCm39)	missense	probably damaging	0.97
R0846:Pdxdc1	UTSW	16	13,672,257 (GRCm39)	critical splice donor site	probably null
R0944:Pdxdc1	UTSW	16	13,656,233 (GRCm39)	missense	probably damaging	1.00
R0945:Pdxdc1	UTSW	16	13,675,296 (GRCm39)	missense	probably damaging	1.00
R1118:Pdxdc1	UTSW	16	13,697,278 (GRCm39)	splice site	probably benign
R1726:Pdxdc1	UTSW	16	13,656,164 (GRCm39)	critical splice donor site	probably null
R2425:Pdxdc1	UTSW	16	13,697,372 (GRCm39)	missense	possibly damaging	0.90
R3890:Pdxdc1	UTSW	16	13,654,312 (GRCm39)	missense	probably benign
R4452:Pdxdc1	UTSW	16	13,654,990 (GRCm39)	missense	possibly damaging	0.55
R4516:Pdxdc1	UTSW	16	13,656,210 (GRCm39)	nonsense	probably null
R4938:Pdxdc1	UTSW	16	13,693,933 (GRCm39)	missense	probably benign	0.03
R5352:Pdxdc1	UTSW	16	13,658,175 (GRCm39)	missense	probably benign	0.01
R5554:Pdxdc1	UTSW	16	13,690,363 (GRCm39)	missense	probably benign	0.01
R7300:Pdxdc1	UTSW	16	13,697,374 (GRCm39)	missense	probably damaging	0.99
R7356:Pdxdc1	UTSW	16	13,677,867 (GRCm39)	missense	probably damaging	1.00
R7963:Pdxdc1	UTSW	16	13,694,030 (GRCm39)	missense	possibly damaging	0.93
R8930:Pdxdc1	UTSW	16	13,672,269 (GRCm39)	missense	probably damaging	1.00
R8932:Pdxdc1	UTSW	16	13,672,269 (GRCm39)	missense	probably damaging	1.00
Z1176:Pdxdc1	UTSW	16	13,720,907 (GRCm39)	unclassified	probably benign

Predicted Primers

PCR Primer
(F):5'- TCAGTCAAGGGCAATATTACGG -3'
(R):5'- AACACAGCCAGCTCTTTGAG -3'

Sequencing Primer
(F):5'- GGGCAATATTACGGACCATCTC -3'
(R):5'- AGCATCTGACACGTTCTATGTG -3'

Posted On

2017-01-24