Mutagenetix > Incidental Mutation

Incidental Mutation 'IGL02884:Pdxdc1'

362935

Institutional Source

Australian Phenomics Network (link to record)

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: 0.192) question?

Stock #

IGL02884

Quality Score

Status

Chromosome

Chromosomal Location

13651012-13720995 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 13661659 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Phenylalanine to Leucine at position 459 (F459L)

Ref Sequence

ENSEMBL: ENSMUSP00000023361 (fasta)

Gene Model

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

AlphaFold

no structure available at present

Predicted Effect

possibly damaging
Transcript: ENSMUST00000023361
AA Change: F459L

PolyPhen 2 Score 0.863 (Sensitivity: 0.83; Specificity: 0.93)

SMART Domains

Protein: ENSMUSP00000023361
Gene: ENSMUSG00000022680
AA Change: F459L

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: ENSMUST00000115803

SMART Domains

Protein: ENSMUSP00000111469
Gene: ENSMUSG00000022680

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

Predicted Effect

possibly damaging
Transcript: ENSMUST00000115804
AA Change: F459L

PolyPhen 2 Score 0.810 (Sensitivity: 0.84; Specificity: 0.93)

SMART Domains

Protein: ENSMUSP00000111471
Gene: ENSMUSG00000022680
AA Change: F459L

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: ENSMUST00000124860

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000127432

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000144913

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000150435

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000154150

Coding Region Coverage

Validation Efficiency

Allele List at MGI

Other mutations in this stock

Total: 53 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4930438A08Rik	A	G	11: 58,178,302 (GRCm39)	I121V	probably benign	Het
Adprh	C	T	16: 38,266,396 (GRCm39)	V249I	probably benign	Het
Akap11	A	T	14: 78,736,402 (GRCm39)	M1797K	probably benign	Het
Akap6	T	A	12: 52,933,405 (GRCm39)	I299N	probably benign	Het
Akr1c12	A	T	13: 4,322,211 (GRCm39)	M277K	possibly damaging	Het
Ankrd17	A	T	5: 90,412,616 (GRCm39)	M1236K	probably damaging	Het
Arhgef11	A	G	3: 87,635,313 (GRCm39)	D874G	probably damaging	Het
Atg4b	T	C	1: 93,715,437 (GRCm39)		probably benign	Het
Bcl9	G	A	3: 97,117,368 (GRCm39)	P442L	probably damaging	Het
Ccdc107	A	T	4: 43,495,228 (GRCm39)	K98*	probably null	Het
Cenpl	A	G	1: 160,913,619 (GRCm39)	Q343R	probably benign	Het
Cep104	T	C	4: 154,074,319 (GRCm39)	C524R	probably damaging	Het
Clec3b	C	T	9: 122,985,827 (GRCm39)	T75I	probably benign	Het
Col13a1	A	T	10: 61,741,064 (GRCm39)		probably benign	Het
Crot	C	T	5: 9,028,197 (GRCm39)		probably null	Het
Ddo	G	A	10: 40,513,360 (GRCm39)	V101I	probably benign	Het
Disp2	T	C	2: 118,618,032 (GRCm39)		probably benign	Het
Dnmt3b	A	C	2: 153,516,297 (GRCm39)	Y474S	probably damaging	Het
Dpp6	T	A	5: 27,839,554 (GRCm39)	N298K	possibly damaging	Het
Fbf1	C	T	11: 116,037,339 (GRCm39)	E940K	probably damaging	Het
Fgd6	A	G	10: 93,881,501 (GRCm39)		probably benign	Het
H2-M10.2	T	C	17: 36,595,568 (GRCm39)	R241G	probably damaging	Het
Haghl	A	T	17: 26,002,072 (GRCm39)	F207Y	possibly damaging	Het
Helt	G	A	8: 46,745,620 (GRCm39)	R88C	probably damaging	Het
Igf2bp2	T	C	16: 21,981,635 (GRCm39)	K27E	probably benign	Het
Il1b	T	C	2: 129,207,022 (GRCm39)	H246R	probably benign	Het
Itprid1	T	C	6: 55,851,339 (GRCm39)		probably null	Het
Kcnu1	C	T	8: 26,411,556 (GRCm39)	S167L	probably damaging	Het
Kif16b	A	T	2: 142,544,534 (GRCm39)		probably benign	Het
Myh7	A	T	14: 55,230,276 (GRCm39)	S19T	probably benign	Het
Ncaph2	T	C	15: 89,248,447 (GRCm39)		probably null	Het
Nlrp4c	T	C	7: 6,101,951 (GRCm39)	L879P	probably damaging	Het
Nqo2	T	A	13: 34,156,344 (GRCm39)	N19K	probably damaging	Het
Or2r2	C	T	6: 42,463,540 (GRCm39)	V196M	probably damaging	Het
Osbpl1a	C	A	18: 12,952,635 (GRCm39)	G93*	probably null	Het
Phc2	A	T	4: 128,601,809 (GRCm39)	H88L	probably damaging	Het
Pkd1l2	G	A	8: 117,792,484 (GRCm39)	T436I	probably benign	Het
Ptchd4	A	T	17: 42,813,340 (GRCm39)	T414S	possibly damaging	Het
Rab7b	A	G	1: 131,626,280 (GRCm39)	R103G	probably damaging	Het
Retnla	A	G	16: 48,662,943 (GRCm39)	Y3C	probably benign	Het
Samd7	G	A	3: 30,810,322 (GRCm39)	R113H	probably damaging	Het
Shisa9	G	A	16: 11,814,907 (GRCm39)		probably benign	Het
Soat1	A	T	1: 156,268,926 (GRCm39)	I208N	possibly damaging	Het
Stab1	C	A	14: 30,872,100 (GRCm39)		probably null	Het
Tti2	C	T	8: 31,641,505 (GRCm39)	L210F	possibly damaging	Het
Ube2v2	A	G	16: 15,374,349 (GRCm39)	V77A	probably benign	Het
Ubr5	T	C	15: 37,998,620 (GRCm39)	E1617G	probably damaging	Het
Vmn2r16	T	A	5: 109,508,757 (GRCm39)	I495K	possibly damaging	Het
Vwce	G	T	19: 10,623,943 (GRCm39)	R278L	possibly damaging	Het
Wdr26	C	T	1: 181,010,349 (GRCm39)	A551T	probably damaging	Het
Wee1	A	G	7: 109,725,269 (GRCm39)	I304V	probably benign	Het
Xrcc5	C	T	1: 72,385,396 (GRCm39)	H496Y	possibly damaging	Het
Zfp142	G	T	1: 74,611,142 (GRCm39)	S884R	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
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
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

Posted On

2015-12-18