Mutagenetix > Incidental Mutation

Incidental Mutation 'IGL02954:Pdcd5'

365053

Institutional Source

Australian Phenomics Network (link to record)

Gene Symbol

Pdcd5

Ensembl Gene

ENSMUSG00000030417

Gene Name

programmed cell death 5

Synonyms

2200003D22Rik, Tfar19

Accession Numbers

Essential gene?

Probably essential (E-score: 0.960) question?

Stock #

IGL02954

Quality Score

Status

Chromosome

Chromosomal Location

35341410-35346907 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 35343089 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Tyrosine to Cysteine at position 152 (Y152C)

Ref Sequence

ENSEMBL: ENSMUSP00000113013 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000040844] [ENSMUST00000118501] [ENSMUST00000120714] [ENSMUST00000190503]

AlphaFold

P56812

Predicted Effect

probably benign
Transcript: ENSMUST00000040844

SMART Domains

Protein: ENSMUSP00000041751
Gene: ENSMUSG00000034867

Domain	Start	End	E-Value	Type
Blast:ANK	8	37	2e-8	BLAST
VPS9	264	380	1.92e-7	SMART
Blast:ANK	393	418	8e-9	BLAST
low complexity region	419	430	N/A	INTRINSIC
ANK	462	491	8.65e-5	SMART
ANK	495	524	1.8e-2	SMART
ANK	528	558	2.45e-4	SMART
ANK	564	593	6.46e-4	SMART
low complexity region	638	658	N/A	INTRINSIC
ANK	742	774	8.39e-3	SMART
ANK	775	804	5.93e-3	SMART
ANK	808	837	4.46e-7	SMART
ANK	841	870	2.81e-4	SMART

Predicted Effect

probably damaging
Transcript: ENSMUST00000118501
AA Change: Y73C

PolyPhen 2 Score 0.982 (Sensitivity: 0.75; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000113761
Gene: ENSMUSG00000030417
AA Change: Y73C

Domain	Start	End	E-Value	Type
Pfam:dsDNA_bind	9	113	9.6e-38	PFAM

Predicted Effect

probably damaging
Transcript: ENSMUST00000120714
AA Change: Y152C

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000113013
Gene: ENSMUSG00000030417
AA Change: Y152C

Domain	Start	End	E-Value	Type
low complexity region	9	26	N/A	INTRINSIC
low complexity region	29	39	N/A	INTRINSIC
low complexity region	56	64	N/A	INTRINSIC
Pfam:dsDNA_bind	91	192	1.9e-34	PFAM

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000126734

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000127213

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000130306

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000130340

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000151336

Predicted Effect

probably benign
Transcript: ENSMUST00000190503

SMART Domains

Protein: ENSMUSP00000140259
Gene: ENSMUSG00000034867

Domain	Start	End	E-Value	Type
Blast:ANK	8	37	2e-8	BLAST
VPS9	264	380	1.92e-7	SMART
Blast:ANK	393	418	7e-9	BLAST
low complexity region	419	430	N/A	INTRINSIC
ANK	462	491	8.65e-5	SMART
ANK	495	524	1.8e-2	SMART
ANK	528	558	2.45e-4	SMART
ANK	564	593	6.46e-4	SMART
low complexity region	638	658	N/A	INTRINSIC
ANK	687	719	8.39e-3	SMART
ANK	720	749	5.93e-3	SMART
ANK	753	782	4.46e-7	SMART
ANK	786	815	2.81e-4	SMART

Coding Region Coverage

Validation Efficiency

Allele List at MGI

Other mutations in this stock

Total: 39 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abcb1a	G	T	5: 8,782,341 (GRCm39)	R908L	probably benign	Het
Abcc9	T	C	6: 142,592,007 (GRCm39)	N774S	probably damaging	Het
Alpk2	C	T	18: 65,439,207 (GRCm39)	V729I	probably benign	Het
Atf3	T	C	1: 190,903,852 (GRCm39)	N125D	probably damaging	Het
Bcat1	C	T	6: 144,964,945 (GRCm39)	G215D	probably damaging	Het
Bptf	G	T	11: 106,945,575 (GRCm39)	Q2555K	possibly damaging	Het
Cthrc1	A	G	15: 38,940,389 (GRCm39)		probably benign	Het
Cyp2c38	A	G	19: 39,379,520 (GRCm39)	M443T	probably damaging	Het
D6Wsu163e	C	T	6: 126,951,441 (GRCm39)		probably benign	Het
Dgkg	T	A	16: 22,441,003 (GRCm39)	E3D	probably benign	Het
Dnah8	G	T	17: 30,923,809 (GRCm39)	R1259L	probably benign	Het
Dnah9	A	G	11: 66,009,793 (GRCm39)	L698P	probably damaging	Het
Ebag9	A	C	15: 44,493,601 (GRCm39)	H141P	probably benign	Het
Emilin2	T	C	17: 71,563,526 (GRCm39)	R840G	probably benign	Het
Faap100	A	T	11: 120,262,957 (GRCm39)	H800Q	probably damaging	Het
Fh1	A	T	1: 175,437,301 (GRCm39)	I266N	probably damaging	Het
Fkbp15	A	G	4: 62,239,302 (GRCm39)		probably benign	Het
Gm17334	A	G	11: 53,663,654 (GRCm39)		probably benign	Het
Gm5773	G	T	3: 93,680,358 (GRCm39)	W10L	probably benign	Het
Gng13	T	C	17: 25,937,726 (GRCm39)	Y18H	probably damaging	Het
Hivep3	T	C	4: 119,990,838 (GRCm39)	S2113P	probably damaging	Het
Ift81	A	T	5: 122,748,248 (GRCm39)		probably benign	Het
Irak3	A	C	10: 120,012,147 (GRCm39)	L206V	probably damaging	Het
Kcng4	C	T	8: 120,359,792 (GRCm39)	A195T	probably benign	Het
Lrrc40	G	A	3: 157,747,302 (GRCm39)		probably benign	Het
Nars2	T	G	7: 96,689,100 (GRCm39)		probably null	Het
Nol8	T	C	13: 49,814,648 (GRCm39)	V234A	probably benign	Het
Or12j4	A	T	7: 140,046,353 (GRCm39)	K80*	probably null	Het
Or1o4	T	A	17: 37,591,195 (GRCm39)	N39Y	probably damaging	Het
Patz1	A	G	11: 3,241,761 (GRCm39)	Y383C	probably damaging	Het
Phkg1	A	G	5: 129,894,910 (GRCm39)	W214R	probably damaging	Het
Plxna1	A	G	6: 89,301,649 (GRCm39)	L1459P	probably damaging	Het
Pspc1	G	A	14: 57,009,217 (GRCm39)	P206S	probably benign	Het
St7	A	T	6: 17,848,030 (GRCm39)	N198I	probably damaging	Het
Supt3	A	G	17: 45,349,015 (GRCm39)	D249G	probably damaging	Het
Taf1c	T	C	8: 120,327,225 (GRCm39)	Y418C	probably damaging	Het
Tdrd6	A	G	17: 43,938,153 (GRCm39)	V965A	possibly damaging	Het
Ugt2b35	A	G	5: 87,159,180 (GRCm39)	N458S	probably benign	Het
Vmn1r8	A	G	6: 57,013,315 (GRCm39)	Y122C	probably benign	Het

Other mutations in Pdcd5

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL02447:Pdcd5	APN	7	35,342,110 (GRCm39)	missense	possibly damaging	0.95
R0825:Pdcd5	UTSW	7	35,346,338 (GRCm39)	missense	possibly damaging	0.75
R4426:Pdcd5	UTSW	7	35,345,605 (GRCm39)	missense	possibly damaging	0.49
R4614:Pdcd5	UTSW	7	35,346,472 (GRCm39)	intron	probably benign
R4860:Pdcd5	UTSW	7	35,343,135 (GRCm39)	missense	possibly damaging	0.50
R4860:Pdcd5	UTSW	7	35,343,135 (GRCm39)	missense	possibly damaging	0.50
R4984:Pdcd5	UTSW	7	35,342,110 (GRCm39)	missense	probably damaging	1.00
R5249:Pdcd5	UTSW	7	35,346,421 (GRCm39)	intron	probably benign
R5682:Pdcd5	UTSW	7	35,346,613 (GRCm39)	start gained	probably benign
R6384:Pdcd5	UTSW	7	35,346,334 (GRCm39)	missense	possibly damaging	0.60
R6787:Pdcd5	UTSW	7	35,342,063 (GRCm39)	missense	probably damaging	0.99
R8896:Pdcd5	UTSW	7	35,346,795 (GRCm39)	start codon destroyed	probably null	0.84
R9469:Pdcd5	UTSW	7	35,343,827 (GRCm39)	missense	probably benign	0.00

Posted On

2015-12-18