Mutagenetix > Incidental Mutation

Incidental Mutation 'R5554:Pdxdc1'

435314

Institutional Source

Beutler Lab

Gene Symbol

Pdxdc1

Ensembl Gene

ENSMUSG00000022680

Gene Name

pyridoxal-dependent decarboxylase domain containing 1

Synonyms

2210010A19Rik

MMRRC Submission

043111-MU

Accession Numbers

Essential gene?

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

Stock #

R5554 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

13651012-13720995 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to T at 13690363 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Cysteine to Serine at position 202 (C202S)

Ref Sequence

ENSEMBL: ENSMUSP00000111468 (fasta)

Gene Model

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

AlphaFold

no structure available at present

Predicted Effect

probably benign
Transcript: ENSMUST00000023361
AA Change: C202S

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

SMART Domains

Protein: ENSMUSP00000023361
Gene: ENSMUSG00000022680
AA Change: C202S

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

probably benign
Transcript: ENSMUST00000115802
AA Change: C202S

PolyPhen 2 Score 0.015 (Sensitivity: 0.96; Specificity: 0.79)

SMART Domains

Protein: ENSMUSP00000111468
Gene: ENSMUSG00000022680
AA Change: C202S

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

Predicted Effect

probably benign
Transcript: ENSMUST00000115803

SMART Domains

Protein: ENSMUSP00000111469
Gene: ENSMUSG00000022680

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

Predicted Effect

probably benign
Transcript: ENSMUST00000115804
AA Change: C202S

PolyPhen 2 Score 0.012 (Sensitivity: 0.96; Specificity: 0.78)

SMART Domains

Protein: ENSMUSP00000111471
Gene: ENSMUSG00000022680
AA Change: C202S

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: ENSMUST00000151774

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000154150

Meta Mutation Damage Score

0.1497

Coding Region Coverage

1x: 99.9%
3x: 99.7%
10x: 98.6%
20x: 96.1%

Validation Efficiency

97% (73/75)

Allele List at MGI

Other mutations in this stock

Total: 68 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Aarsd1	C	A	11: 101,304,807 (GRCm39)	R227L	probably benign	Het
Adamtsl1	A	G	4: 86,195,182 (GRCm39)	Q533R	possibly damaging	Het
Adgb	C	T	10: 10,216,217 (GRCm39)	R1524H	probably damaging	Het
Ank2	A	T	3: 126,792,622 (GRCm39)	N739K	possibly damaging	Het
Ankrd39	C	T	1: 36,581,062 (GRCm39)	G96R	probably damaging	Het
Anxa10	G	A	8: 62,514,080 (GRCm39)	P249L	possibly damaging	Het
Banp	G	A	8: 122,718,334 (GRCm39)	E183K	probably damaging	Het
BC051665	C	G	13: 60,932,435 (GRCm39)	L83F	probably damaging	Het
Btn1a1	A	T	13: 23,643,295 (GRCm39)	F385I	possibly damaging	Het
Chchd4	A	T	6: 91,441,999 (GRCm39)	*140R	probably null	Het
Dcpp2	T	C	17: 24,119,545 (GRCm39)	Y120H	probably damaging	Het
Dlx2	G	A	2: 71,375,805 (GRCm39)	R173C	possibly damaging	Het
Dmbt1	C	A	7: 130,701,030 (GRCm39)	Y1069*	probably null	Het
Dop1a	T	A	9: 86,403,710 (GRCm39)	F1637I	probably damaging	Het
Dusp18	T	C	11: 3,847,202 (GRCm39)	I64T	probably damaging	Het
Evi5l	A	G	8: 4,256,491 (GRCm39)		probably benign	Het
Fiz1	T	C	7: 5,015,849 (GRCm39)	H47R	probably damaging	Het
Fndc3b	G	T	3: 27,697,162 (GRCm39)	P17T	possibly damaging	Het
Foxa1	T	A	12: 57,589,077 (GRCm39)	Q381L	probably benign	Het
Gda	A	G	19: 21,405,837 (GRCm39)		probably null	Het
Gm10044	T	C	14: 7,771,181 (GRCm38)		noncoding transcript	Het
Gm12258	T	A	11: 58,749,294 (GRCm39)	S156R	possibly damaging	Het
Gm973	A	G	1: 59,566,131 (GRCm39)	R117G	probably benign	Het
Grwd1	C	T	7: 45,480,064 (GRCm39)	V48I	probably damaging	Het
Ifi209	T	A	1: 173,468,763 (GRCm39)	S198T	probably benign	Het
Inka2	T	A	3: 105,623,930 (GRCm39)	S82R	possibly damaging	Het
Itga1	A	T	13: 115,129,010 (GRCm39)	C549*	probably null	Het
Kmt2c	C	A	5: 25,499,608 (GRCm39)	G511C	probably damaging	Het
Knstrn	T	C	2: 118,664,444 (GRCm39)		probably benign	Het
Lrp2	T	C	2: 69,382,768 (GRCm39)	Y39C	possibly damaging	Het
Maco1	T	C	4: 134,555,445 (GRCm39)	I343V	probably benign	Het
Micos10	T	C	4: 138,833,218 (GRCm39)		probably benign	Het
N4bp2	T	C	5: 65,965,457 (GRCm39)	Y1169H	probably benign	Het
Nbr1	C	T	11: 101,455,633 (GRCm39)	T129I	probably benign	Het
Or52e8	A	C	7: 104,625,189 (GRCm39)	M1R	probably null	Het
Or5k15	A	T	16: 58,710,169 (GRCm39)	M138K	possibly damaging	Het
Or7g25	T	C	9: 19,160,039 (GRCm39)	I219V	probably benign	Het
Oxct1	T	A	15: 4,120,677 (GRCm39)	F254I	probably benign	Het
Patj	T	A	4: 98,342,633 (GRCm39)	S576T	possibly damaging	Het
Pet100	A	T	8: 3,672,381 (GRCm39)	I19F	probably damaging	Het
Pik3r5	T	C	11: 68,385,059 (GRCm39)	Y655H	probably damaging	Het
Pkhd1	A	G	1: 20,151,476 (GRCm39)	S3807P	probably damaging	Het
Ptma	A	G	1: 86,454,649 (GRCm39)	T8A	probably damaging	Het
Ptpn3	G	T	4: 57,240,843 (GRCm39)	N257K	probably damaging	Het
R3hdm1	C	A	1: 128,164,409 (GRCm39)	Q1108K	probably benign	Het
Rimbp2	T	C	5: 128,857,406 (GRCm39)	D815G	probably damaging	Het
Scn10a	A	G	9: 119,523,196 (GRCm39)	F66L	probably benign	Het
Selenot	T	C	3: 58,484,296 (GRCm39)		probably null	Het
Serpinb8	A	G	1: 107,526,705 (GRCm39)	T82A	probably benign	Het
Serpini2	G	A	3: 75,175,295 (GRCm39)		probably benign	Het
Slc1a6	G	T	10: 78,631,816 (GRCm39)	G214V	probably benign	Het
Slc5a6	C	A	5: 31,195,444 (GRCm39)	A425S	probably damaging	Het
Smo	C	A	6: 29,736,123 (GRCm39)	N38K	possibly damaging	Het
Smtn	A	T	11: 3,470,811 (GRCm39)	C909*	probably null	Het
Sntg2	C	T	12: 30,308,040 (GRCm39)	R215H	probably benign	Het
Stk4	T	A	2: 163,941,645 (GRCm39)	V287E	probably benign	Het
Tdrd7	A	G	4: 46,005,358 (GRCm39)	D388G	possibly damaging	Het
Ttn	A	T	2: 76,642,652 (GRCm39)	F13294L	probably damaging	Het
Ube2j1	T	G	4: 33,040,745 (GRCm39)	F84V	probably damaging	Het
Ugt3a1	A	G	15: 9,370,287 (GRCm39)	Q477R	probably damaging	Het
Utf1	T	C	7: 139,523,859 (GRCm39)	S25P	probably benign	Het
Vmn1r184	A	T	7: 25,966,413 (GRCm39)	H53L	probably damaging	Het
Vmn2r13	A	T	5: 109,339,860 (GRCm39)	N38K	possibly damaging	Het
Vps13a	C	T	19: 16,699,775 (GRCm39)	D756N	probably damaging	Het
Vwa1	G	T	4: 155,857,695 (GRCm39)	D34E	probably damaging	Het
Zfhx2	A	C	14: 55,301,774 (GRCm39)	L2070R	probably damaging	Het
Zfp984	A	G	4: 147,840,362 (GRCm39)	V163A	probably benign	Het
Zp3r	A	T	1: 130,511,208 (GRCm39)	M325K	probably benign	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
IGL02991:Pdxdc1	UTSW	16	13,675,260 (GRCm39)	missense	probably damaging	1.00
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
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'- GCCTGGCCTTCATTCAGATAC -3'
(R):5'- AAACTTGAGGTCTTGAGGGG -3'

Sequencing Primer
(F):5'- CTGGCCTTCATTCAGATACAAAGG -3'
(R):5'- TAGGCCAGGCTGACTTCATACATG -3'

Posted On

2016-10-24