Mutagenetix > Incidental Mutation

Incidental Mutation 'R5352:Pdxdc1'

423867

Institutional Source

Beutler Lab

Gene Symbol

Pdxdc1

Ensembl Gene

ENSMUSG00000022680

Gene Name

pyridoxal-dependent decarboxylase domain containing 1

Synonyms

2210010A19Rik

MMRRC Submission

042931-MU

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.131) question?

Stock #

R5352 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

13833148-13903131 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 13840311 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Asparagine to Serine at position 516 (N516S)

Ref Sequence

ENSEMBL: ENSMUSP00000023361 (fasta)

Gene Model

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

AlphaFold

no structure available at present

Predicted Effect

probably benign
Transcript: ENSMUST00000023361
AA Change: N516S

PolyPhen 2 Score 0.010 (Sensitivity: 0.96; Specificity: 0.77)

SMART Domains

Protein: ENSMUSP00000023361
Gene: ENSMUSG00000022680
AA Change: N516S

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 benign
Transcript: ENSMUST00000115804
AA Change: N516S

PolyPhen 2 Score 0.009 (Sensitivity: 0.96; Specificity: 0.77)

SMART Domains

Protein: ENSMUSP00000111471
Gene: ENSMUSG00000022680
AA Change: N516S

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: ENSMUST00000148848

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000150435

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000152450

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000154150

Meta Mutation Damage Score

0.0604

Coding Region Coverage

1x: 99.3%
3x: 98.7%
10x: 97.5%
20x: 95.9%

Validation Efficiency

100% (66/66)

Allele List at MGI

Other mutations in this stock

Total: 57 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
A630010A05Rik	T	G	16: 14,618,701	L206*	probably null	Het
Adgrv1	T	C	13: 81,494,657	Y3218C	probably damaging	Het
Agtpbp1	G	A	13: 59,473,746	T41M	probably damaging	Het
Akap6	A	T	12: 52,796,097	E76V	probably damaging	Het
Ank2	C	A	3: 127,498,991		probably benign	Het
Atp6ap1l	A	C	13: 90,883,756	L269R	probably damaging	Het
Blk	A	G	14: 63,375,971	S363P	probably damaging	Het
Btnl9	T	C	11: 49,178,840	N204S	probably benign	Het
Cc2d2a	G	T	5: 43,706,213	W672C	probably damaging	Het
Ccnf	A	G	17: 24,243,273		probably null	Het
Cdc45	C	T	16: 18,795,897	R205H	probably damaging	Het
Chst1	A	G	2: 92,613,365	T61A	possibly damaging	Het
Col6a4	G	A	9: 106,061,544	T1325I	probably damaging	Het
Col7a1	A	C	9: 108,961,411	T976P	unknown	Het
Corin	C	T	5: 72,305,033	S811N	probably benign	Het
Dnal1	T	C	12: 84,136,548	V27A	possibly damaging	Het
Dupd1	G	A	14: 21,677,023	R186W	probably benign	Het
F830045P16Rik	T	A	2: 129,472,901	H152L	probably damaging	Het
Flnc	A	G	6: 29,449,318	S1405G	possibly damaging	Het
Foxj1	T	C	11: 116,334,079	N154S	possibly damaging	Het
Gm12183	T	C	11: 48,752,162		noncoding transcript	Het
Gm27047	G	A	6: 130,631,019		noncoding transcript	Het
Grm5	A	G	7: 88,074,850	I783V	probably damaging	Het
Hk1	A	T	10: 62,304,770	S113T	probably damaging	Het
Iqca	A	T	1: 90,130,196	N260K	probably benign	Het
Iws1	A	T	18: 32,083,404	K399M	probably damaging	Het
Kdm4d	A	G	9: 14,464,358	I68T	probably damaging	Het
Man2a1	T	C	17: 64,731,246	I75T	probably damaging	Het
Med13	T	A	11: 86,301,468	I824L	possibly damaging	Het
Meioc	A	T	11: 102,675,313	E585V	probably benign	Het
Mrgpre	A	C	7: 143,781,094	F224C	probably damaging	Het
Muc5b	T	A	7: 141,864,558	F3747Y	possibly damaging	Het
Nlrp4e	T	C	7: 23,353,173	V839A	probably benign	Het
Nup210	A	T	6: 91,069,316	V545E	probably damaging	Het
Ola1	T	C	2: 73,099,330	T310A	probably damaging	Het
Phlpp1	A	G	1: 106,172,725	D241G	probably benign	Het
Ppp1r36	T	C	12: 76,428,083	V85A	probably damaging	Het
Rasa3	A	C	8: 13,631,778	L57R	possibly damaging	Het
Rp1	T	C	1: 4,347,098	S1264G	probably benign	Het
Rprd1b	A	G	2: 158,058,736	E247G	probably damaging	Het
Sag	G	T	1: 87,812,993	V46L	probably benign	Het
Sat2	A	T	11: 69,622,315	I17F	probably damaging	Het
Slc39a6	A	T	18: 24,601,036	Y199N	probably benign	Het
Slc9a3r2	C	T	17: 24,642,255	R66H	probably damaging	Het
Snx2	A	G	18: 53,197,925		probably null	Het
Thbs4	T	C	13: 92,763,590	D466G	probably damaging	Het
Tmem208	A	G	8: 105,328,431	D91G	probably damaging	Het
Tmf1	A	G	6: 97,176,809	L101P	probably damaging	Het
Tnni1	A	G	1: 135,805,592	T51A	probably benign	Het
Tor3a	T	G	1: 156,674,193	E38A	probably damaging	Het
Trim31	T	A	17: 36,899,918	D147E	possibly damaging	Het
Uhrf1bp1	G	A	17: 27,887,515	S1005N	probably benign	Het
Vmn1r48	G	T	6: 90,036,147	A232E	probably benign	Het
Vmn1r89	T	G	7: 13,219,357	F7V	probably benign	Het
Zfp160	A	G	17: 21,026,852	T555A	probably benign	Het
Zfp981	C	A	4: 146,537,005	T129K	probably benign	Het
Zfpm2	T	A	15: 40,870,542	F106I	probably benign	Het

Other mutations in Pdxdc1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01760:Pdxdc1	APN	16	13859152	missense	probably damaging	1.00
IGL02101:Pdxdc1	APN	16	13869856	missense	probably damaging	0.99
IGL02484:Pdxdc1	APN	16	13876081	missense	possibly damaging	0.94
IGL02523:Pdxdc1	APN	16	13881935	missense	probably damaging	1.00
IGL02560:Pdxdc1	APN	16	13839732	missense	probably benign	0.00
IGL02884:Pdxdc1	APN	16	13843795	missense	possibly damaging	0.86
IGL03008:Pdxdc1	APN	16	13876159	missense	possibly damaging	0.81
IGL03162:Pdxdc1	APN	16	13857417	missense	probably damaging	0.99
IGL02991:Pdxdc1	UTSW	16	13857396	missense	probably damaging	1.00
PIT4472001:Pdxdc1	UTSW	16	13845345	missense	probably damaging	1.00
R0015:Pdxdc1	UTSW	16	13887683	splice site	probably benign
R0240:Pdxdc1	UTSW	16	13879445	missense	probably damaging	1.00
R0240:Pdxdc1	UTSW	16	13879445	missense	probably damaging	1.00
R0432:Pdxdc1	UTSW	16	13854400	missense	probably damaging	0.97
R0846:Pdxdc1	UTSW	16	13854393	critical splice donor site	probably null
R0944:Pdxdc1	UTSW	16	13838369	missense	probably damaging	1.00
R0945:Pdxdc1	UTSW	16	13857432	missense	probably damaging	1.00
R1118:Pdxdc1	UTSW	16	13879414	splice site	probably benign
R1726:Pdxdc1	UTSW	16	13838300	critical splice donor site	probably null
R2425:Pdxdc1	UTSW	16	13879508	missense	possibly damaging	0.90
R3890:Pdxdc1	UTSW	16	13836448	missense	probably benign
R4452:Pdxdc1	UTSW	16	13837126	missense	possibly damaging	0.55
R4516:Pdxdc1	UTSW	16	13838346	nonsense	probably null
R4938:Pdxdc1	UTSW	16	13876069	missense	probably benign	0.03
R5554:Pdxdc1	UTSW	16	13872499	missense	probably benign	0.01
R7300:Pdxdc1	UTSW	16	13879510	missense	probably damaging	0.99
R7356:Pdxdc1	UTSW	16	13860003	missense	probably damaging	1.00
R7963:Pdxdc1	UTSW	16	13876166	missense	possibly damaging	0.93
R8930:Pdxdc1	UTSW	16	13854405	missense	probably damaging	1.00
R8932:Pdxdc1	UTSW	16	13854405	missense	probably damaging	1.00
Z1176:Pdxdc1	UTSW	16	13903043	unclassified	probably benign

Predicted Primers

PCR Primer
(F):5'- AATGAACCCTGCCGAAGTC -3'
(R):5'- TGAGAGTCACCCAGTCATCC -3'

Sequencing Primer
(F):5'- TGCCGAAGTCCAATGCTG -3'
(R):5'- GAGAGTCACCCAGTCATCCTTTAATC -3'

Posted On

2016-08-04