Mutagenetix > Incidental Mutation

Incidental Mutation 'R1118:Pdxdc1'

97613

Institutional Source

Beutler Lab

Gene Symbol

Pdxdc1

Ensembl Gene

ENSMUSG00000022680

Gene Name

pyridoxal-dependent decarboxylase domain containing 1

Synonyms

2210010A19Rik

MMRRC Submission

039191-MU

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.192) question?

Stock #

R1118 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

13651012-13720995 bp(-) (GRCm39)

Type of Mutation

splice site

DNA Base Change (assembly)

T to A at 13697278 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Ref Sequence

ENSEMBL: ENSMUSP00000111471 (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

SMART Domains

Protein: ENSMUSP00000023361
Gene: ENSMUSG00000022680

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

SMART Domains

Protein: ENSMUSP00000111468
Gene: ENSMUSG00000022680

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

SMART Domains

Protein: ENSMUSP00000111471
Gene: ENSMUSG00000022680

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: ENSMUST00000148551

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000151774

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000154150

Coding Region Coverage

1x: 99.2%
3x: 98.4%
10x: 96.7%
20x: 94.3%

Validation Efficiency

98% (60/61)

Allele List at MGI

Other mutations in this stock

Total: 60 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Apcdd1	A	G	18: 63,085,095 (GRCm39)	T431A	probably benign	Het
Bcan	T	A	3: 87,896,534 (GRCm39)	I721F	probably damaging	Het
Card10	T	C	15: 78,686,643 (GRCm39)	D58G	possibly damaging	Het
Cd200r2	A	G	16: 44,729,969 (GRCm39)	N171S	probably damaging	Het
Celsr1	T	C	15: 85,916,248 (GRCm39)	D575G	probably damaging	Het
Ces1f	A	G	8: 93,993,870 (GRCm39)		probably benign	Het
Cped1	A	T	6: 22,237,698 (GRCm39)	H938L	probably benign	Het
Creld1	A	G	6: 113,468,656 (GRCm39)	D259G	probably benign	Het
Cubn	T	C	2: 13,341,053 (GRCm39)	I2223V	possibly damaging	Het
Dop1a	A	G	9: 86,397,459 (GRCm39)	D921G	probably damaging	Het
Dusp7	T	C	9: 106,250,849 (GRCm39)	S325P	possibly damaging	Het
Fat4	A	T	3: 39,037,091 (GRCm39)	D3581V	possibly damaging	Het
Fhl3	T	C	4: 124,599,584 (GRCm39)		probably null	Het
Gap43	T	C	16: 42,112,167 (GRCm39)	E198G	probably benign	Het
Garin4	G	A	1: 190,896,682 (GRCm39)		probably benign	Het
Grina	T	C	15: 76,132,779 (GRCm39)	F182S	probably damaging	Het
Gsk3b	T	C	16: 38,028,346 (GRCm39)		probably benign	Het
Gtf3c3	C	T	1: 54,456,937 (GRCm39)	A488T	probably damaging	Het
Haus6	A	G	4: 86,503,563 (GRCm39)		probably null	Het
Hmcn1	C	T	1: 150,494,679 (GRCm39)	A4137T	possibly damaging	Het
Itih4	C	A	14: 30,618,124 (GRCm39)		probably benign	Het
Itprid1	T	C	6: 55,866,155 (GRCm39)	F183L	probably damaging	Het
Kif22	A	G	7: 126,631,916 (GRCm39)	S384P	probably benign	Het
Lbr	A	C	1: 181,648,233 (GRCm39)		probably benign	Het
Mei1	G	A	15: 82,000,068 (GRCm39)		probably benign	Het
Misp	T	C	10: 79,662,969 (GRCm39)	V462A	probably benign	Het
Mrgpra3	A	C	7: 47,239,039 (GRCm39)	L296V	possibly damaging	Het
Ndufa9	A	T	6: 126,799,031 (GRCm39)	L362Q	probably damaging	Het
Nlrp9c	A	T	7: 26,083,862 (GRCm39)	D572E	probably benign	Het
Or4f14	T	A	2: 111,743,222 (GRCm39)	T18S	probably benign	Het
Otud4	C	T	8: 80,379,980 (GRCm39)		probably benign	Het
P4ha3	T	C	7: 99,962,535 (GRCm39)	I431T	probably damaging	Het
Pcdhb15	T	A	18: 37,606,815 (GRCm39)	F16I	probably benign	Het
Pcnp	A	G	16: 55,844,754 (GRCm39)	S49P	probably damaging	Het
Pgc	T	A	17: 48,039,828 (GRCm39)		probably null	Het
Phf11a	T	C	14: 59,521,778 (GRCm39)	D131G	probably benign	Het
Prdm2	G	A	4: 142,858,953 (GRCm39)	H1446Y	possibly damaging	Het
Rad54b	T	C	4: 11,563,352 (GRCm39)	S4P	probably damaging	Het
Slc52a2	T	C	15: 76,423,808 (GRCm39)		probably benign	Het
Slc9a4	G	A	1: 40,623,490 (GRCm39)		probably benign	Het
Smad4	T	C	18: 73,773,333 (GRCm39)	D551G	probably benign	Het
Smg7	A	T	1: 152,742,326 (GRCm39)		probably benign	Het
Sned1	G	A	1: 93,209,376 (GRCm39)	V830M	possibly damaging	Het
Sspo	A	G	6: 48,436,352 (GRCm39)	Y1234C	probably damaging	Het
Stab2	A	T	10: 86,721,582 (GRCm39)		probably null	Het
Stk36	A	G	1: 74,671,925 (GRCm39)	E875G	probably benign	Het
Stmn4	T	G	14: 66,591,844 (GRCm39)		probably benign	Het
Tagln3	C	A	16: 45,544,635 (GRCm39)	R12L	probably damaging	Het
Tex14	A	T	11: 87,413,343 (GRCm39)	R1031S	probably benign	Het
Tia1	G	A	6: 86,396,091 (GRCm39)	V96I	probably benign	Het
Ticrr	C	T	7: 79,343,701 (GRCm39)	P1189S	probably benign	Het
Tnxb	G	A	17: 34,904,017 (GRCm39)	V1053M	probably damaging	Het
Tpp2	T	C	1: 44,031,556 (GRCm39)		probably null	Het
Trpm7	A	G	2: 126,664,406 (GRCm39)	M991T	possibly damaging	Het
Ttc3	T	A	16: 94,217,127 (GRCm39)		probably benign	Het
Vcan	G	A	13: 89,853,782 (GRCm39)	P393S	probably damaging	Het
Vmn2r107	G	A	17: 20,576,860 (GRCm39)	R286Q	probably benign	Het
Wdr87-ps	G	A	7: 29,233,669 (GRCm39)		noncoding transcript	Het
Wrap73	A	T	4: 154,236,884 (GRCm39)		probably null	Het
Zfp958	A	T	8: 4,676,169 (GRCm39)	N46Y	possibly 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
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
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'- ggagaggttaagcaacAACTCCAAAGAA -3'
(R):5'- CCACACTTTGAGCATCTTGAGGACATT -3'

Sequencing Primer
(F):5'- tgtctgccattcgcctc -3'
(R):5'- CTGGATCTCTCTGTAGGAGATGAAG -3'

Posted On

2014-01-05