Mutagenetix > Incidental Mutation

Incidental Mutation 'R1726:Pdxdc1'

198176

Institutional Source

Beutler Lab

Gene Symbol

Pdxdc1

Ensembl Gene

ENSMUSG00000022680

Gene Name

pyridoxal-dependent decarboxylase domain containing 1

Synonyms

2210010A19Rik

MMRRC Submission

039758-MU

Accession Numbers

Essential gene?

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

Stock #

R1726 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

13651012-13720995 bp(-) (GRCm39)

Type of Mutation

critical splice donor site (2 bp from exon)

DNA Base Change (assembly)

A to C at 13656164 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Ref Sequence

ENSEMBL: ENSMUSP00000111471 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000023361] [ENSMUST00000023362] [ENSMUST00000115804] [ENSMUST00000115805]

AlphaFold

no structure available at present

Predicted Effect

probably null
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: ENSMUST00000023362

SMART Domains

Protein: ENSMUSP00000023362
Gene: ENSMUSG00000022681

Domain	Start	End	E-Value	Type
Pfam:N_Asn_amidohyd	36	304	1.3e-124	PFAM

Predicted Effect

probably null
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

probably benign
Transcript: ENSMUST00000115805

SMART Domains

Protein: ENSMUSP00000111472
Gene: ENSMUSG00000022681

Domain	Start	End	E-Value	Type
Pfam:N_Asn_amidohyd	32	215	1.4e-82	PFAM

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000124860

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000127432

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000136618

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000144913

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000154150

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000148848

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000152450

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000139161

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000150435

Meta Mutation Damage Score

0.9492

Coding Region Coverage

1x: 97.5%
3x: 96.9%
10x: 95.4%
20x: 92.6%

Validation Efficiency

97% (63/65)

Allele List at MGI

Other mutations in this stock

Total: 62 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abcb5	G	C	12: 118,838,536 (GRCm39)		probably null	Het
Abcb5	A	T	12: 118,871,267 (GRCm39)	S711T	possibly damaging	Het
Acoxl	G	A	2: 127,722,366 (GRCm39)	G216R	probably damaging	Het
Arhgef18	A	T	8: 3,504,228 (GRCm39)	N949I	possibly damaging	Het
Bltp3a	C	A	17: 28,105,225 (GRCm39)		probably null	Het
Brip1	A	T	11: 85,955,740 (GRCm39)	S924R	probably benign	Het
Btf3	C	T	13: 98,452,804 (GRCm39)	M1I	probably null	Het
Ccdc141	A	G	2: 76,938,700 (GRCm39)		probably benign	Het
Ccdc80	A	T	16: 44,916,368 (GRCm39)	T375S	probably benign	Het
Ccl11	A	G	11: 81,952,546 (GRCm39)	K40E	possibly damaging	Het
Chrnb2	A	T	3: 89,668,509 (GRCm39)	C269S	probably damaging	Het
Dgat2	A	G	7: 98,831,623 (GRCm39)	S33P	possibly damaging	Het
Dip2c	A	G	13: 9,625,464 (GRCm39)	D608G	probably damaging	Het
Dnah2	A	T	11: 69,388,715 (GRCm39)	D889E	probably damaging	Het
Dvl2	A	T	11: 69,900,287 (GRCm39)	T694S	probably benign	Het
Elapor1	A	G	3: 108,375,184 (GRCm39)	I561T	possibly damaging	Het
Fbf1	A	G	11: 116,036,280 (GRCm39)	V1100A	probably benign	Het
Galt	G	A	4: 41,756,001 (GRCm39)	W22*	probably null	Het
Garem1	C	A	18: 21,281,319 (GRCm39)	V346L	probably damaging	Het
Gm10277	TC	T	11: 77,676,828 (GRCm39)		probably null	Het
Gm10762	A	T	2: 128,809,135 (GRCm39)		probably benign	Het
Gm21900	A	G	Y: 10,616,358 (GRCm39)		probably null	Het
Gm2663	T	C	6: 40,974,960 (GRCm39)	Y37C	probably damaging	Het
Gm42791	C	A	5: 148,896,311 (GRCm39)		probably benign	Het
Gm5134	C	A	10: 75,828,361 (GRCm39)	P314T	possibly damaging	Het
Gtf3c2	T	C	5: 31,326,467 (GRCm39)	E348G	possibly damaging	Het
H2-T24	T	A	17: 36,326,513 (GRCm39)	M129L	probably benign	Het
Ikzf2	C	A	1: 69,587,847 (GRCm39)	R214L	probably damaging	Het
Insyn2a	T	C	7: 134,500,867 (GRCm39)		probably benign	Het
Itpr3	T	A	17: 27,330,664 (GRCm39)	L1691Q	probably damaging	Het
Kmt2c	C	T	5: 25,520,003 (GRCm39)	G2036R	probably damaging	Het
Lrp10	T	C	14: 54,707,113 (GRCm39)	L650P	probably damaging	Het
Mcm9	G	A	10: 53,413,977 (GRCm39)	P368S	possibly damaging	Het
Mob3b	A	G	4: 34,954,028 (GRCm39)	M214T	probably benign	Het
Mrpl1	T	C	5: 96,371,686 (GRCm39)	V71A	probably benign	Het
Mrpl57	A	G	14: 58,064,092 (GRCm39)	E40G	probably damaging	Het
Mtmr9	A	G	14: 63,774,547 (GRCm39)	V162A	possibly damaging	Het
Nalcn	A	T	14: 123,545,816 (GRCm39)	V1065E	probably damaging	Het
Nemp2	A	G	1: 52,676,554 (GRCm39)	D42G	probably damaging	Het
Npepps	A	G	11: 97,115,495 (GRCm39)	L623P	probably damaging	Het
Olig3	A	G	10: 19,232,482 (GRCm39)	S36G	probably benign	Het
Or10j5	A	G	1: 172,784,658 (GRCm39)	T99A	probably benign	Het
Or11g26	T	A	14: 50,753,636 (GRCm39)		probably null	Het
Or5e1	T	C	7: 108,354,215 (GRCm39)	S51P	probably benign	Het
Pcdhb14	T	A	18: 37,582,647 (GRCm39)	Y584*	probably null	Het
Pcyox1l	T	C	18: 61,830,849 (GRCm39)	Y341C	probably benign	Het
Pias4	A	C	10: 80,991,689 (GRCm39)	V313G	probably damaging	Het
Pkd1	C	T	17: 24,783,150 (GRCm39)	T81M	probably damaging	Het
Ptprm	T	C	17: 67,349,322 (GRCm39)	I40M	probably damaging	Het
Reep6	T	C	10: 80,170,954 (GRCm39)	S277P	probably benign	Het
Shank3	A	G	15: 89,442,189 (GRCm39)	E1694G	probably damaging	Het
Shq1	T	C	6: 100,613,996 (GRCm39)	Y274C	probably benign	Het
Slc12a6	T	A	2: 112,177,771 (GRCm39)	I630N	probably damaging	Het
Slc14a1	T	A	18: 78,159,681 (GRCm39)	N15Y	probably benign	Het
Slc17a4	A	T	13: 24,089,574 (GRCm39)	Y114*	probably null	Het
Slc26a1	C	T	5: 108,821,541 (GRCm39)	G116D	probably damaging	Het
Smg8	G	T	11: 86,971,439 (GRCm39)	Y777*	probably null	Het
Tlr11	A	T	14: 50,598,998 (GRCm39)	H328L	probably benign	Het
Ube2c	G	T	2: 164,613,237 (GRCm39)	A52S	probably damaging	Het
Unc5c	A	G	3: 141,523,864 (GRCm39)	S806G	probably damaging	Het
Zfp874b	A	T	13: 67,622,839 (GRCm39)	I153K	probably damaging	Het
Zkscan2	T	A	7: 123,089,046 (GRCm39)	E408D	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
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
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'- AGACCAGTGAGACATCCTACCTGC -3'
(R):5'- ACAGACCTCTGGGAAAGTGTCACC -3'

Sequencing Primer
(F):5'- GTGAGACATCCTACCTGCTGTTAAG -3'
(R):5'- GTCACCAATGCTGTTGACTATG -3'

Posted On

2014-05-23