Mutagenetix > Incidental Mutation

Incidental Mutation 'R8896:Pdcd5'

678027

Institutional Source

Beutler Lab

Gene Symbol

Pdcd5

Ensembl Gene

ENSMUSG00000030417

Gene Name

programmed cell death 5

Synonyms

2200003D22Rik, Tfar19

MMRRC Submission

068698-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.961) question?

Stock #

R8896 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

35341410-35346907 bp(-) (GRCm39)

Type of Mutation

start codon destroyed

DNA Base Change (assembly)

A to T at 35346795 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Methionine to Lysine at position 1 (M1K)

Ref Sequence

ENSEMBL: ENSMUSP00000113761 (fasta)

Gene Model

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

AlphaFold

P56812

Predicted Effect

probably null
Transcript: ENSMUST00000118501
AA Change: M1K

PolyPhen 2 Score 0.838 (Sensitivity: 0.84; Specificity: 0.93)

SMART Domains

Protein: ENSMUSP00000113761
Gene: ENSMUSG00000030417
AA Change: M1K

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

Predicted Effect

probably benign
Transcript: ENSMUST00000120714

SMART Domains

Protein: ENSMUSP00000113013
Gene: ENSMUSG00000030417

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

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.7%
20x: 99.0%

Validation Efficiency

100% (73/73)

Allele List at MGI

Other mutations in this stock

Total: 73 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Aox4	T	G	1: 58,291,233 (GRCm39)	S784A	probably benign	Het
Ap3d1	T	A	10: 80,552,425 (GRCm39)	H581L	probably benign	Het
Atp11a	T	C	8: 12,899,781 (GRCm39)	Y915H	probably damaging	Het
Atp4b	T	C	8: 13,437,514 (GRCm39)	D213G	probably benign	Het
Bcl11a	A	G	11: 24,113,640 (GRCm39)	S328G	probably benign	Het
Bean1	CT	C	8: 104,908,664 (GRCm39)		probably null	Het
Cadps2	T	A	6: 23,410,876 (GRCm39)	Y685F	probably damaging	Het
Ccdc88b	C	T	19: 6,831,203 (GRCm39)	A580T	probably benign	Het
Cdc42bpa	GACAACA	GACA	1: 179,958,373 (GRCm39)		probably benign	Het
Cep152	A	T	2: 125,408,155 (GRCm39)	V1396D	possibly damaging	Het
Ces1c	T	C	8: 93,833,254 (GRCm39)	I404V	probably benign	Het
Cr2	A	T	1: 194,851,581 (GRCm39)	M137K	possibly damaging	Het
Cyp2d40	T	C	15: 82,644,454 (GRCm39)	Y257C	unknown	Het
Dennd1c	T	A	17: 57,381,512 (GRCm39)	D116V	probably damaging	Het
Dph2	G	A	4: 117,747,575 (GRCm39)	R270*	probably null	Het
Dpp8	A	C	9: 64,985,318 (GRCm39)	H792P	possibly damaging	Het
Dusp29	T	C	14: 21,736,763 (GRCm39)	D113G	probably benign	Het
Efs	T	C	14: 55,157,756 (GRCm39)	E185G	possibly damaging	Het
Eml3	A	G	19: 8,914,056 (GRCm39)	E480G	probably damaging	Het
Fam193a	A	G	5: 34,583,828 (GRCm39)	T336A	probably benign	Het
Fermt1	C	T	2: 132,783,852 (GRCm39)		probably benign	Het
Galnt4	T	A	10: 98,945,955 (GRCm39)	V560D	probably damaging	Het
Gbp2b	C	A	3: 142,309,327 (GRCm39)	T146K	probably damaging	Het
Gbp5	C	T	3: 142,211,308 (GRCm39)	T346I	probably damaging	Het
Glrx	G	T	13: 75,995,317 (GRCm39)	C79F	probably damaging	Het
Glt8d2	T	A	10: 82,490,616 (GRCm39)	T225S	probably damaging	Het
Grm3	A	G	5: 9,562,483 (GRCm39)	F456L	possibly damaging	Het
Gse1	T	G	8: 121,303,185 (GRCm39)	S1109A	unknown	Het
Gstp3	A	T	19: 4,108,573 (GRCm39)	L63Q	probably damaging	Het
Hapln3	G	A	7: 78,767,239 (GRCm39)	R267W	probably benign	Het
Herc4	T	A	10: 63,147,286 (GRCm39)	I801N	possibly damaging	Het
Ido1	G	T	8: 25,077,880 (GRCm39)	D153E	probably benign	Het
Itpr3	G	A	17: 27,337,651 (GRCm39)		probably benign	Het
Kcnj9	T	A	1: 172,153,360 (GRCm39)	S255C	probably damaging	Het
Kpna3	T	C	14: 61,629,294 (GRCm39)	N39D	probably benign	Het
Krt39	A	T	11: 99,409,095 (GRCm39)	S269T	probably damaging	Het
Lfng	G	A	5: 140,598,978 (GRCm39)	V296I	probably benign	Het
Lrit3	T	A	3: 129,585,132 (GRCm39)	I209F	probably damaging	Het
Map4k5	T	A	12: 69,870,275 (GRCm39)	D523V	possibly damaging	Het
Mdn1	C	T	4: 32,678,328 (GRCm39)	P652L	probably benign	Het
Med30	G	A	15: 52,584,516 (GRCm39)	V145I	possibly damaging	Het
Megf6	T	A	4: 154,326,860 (GRCm39)	D163E	probably damaging	Het
Meltf	T	A	16: 31,709,522 (GRCm39)		probably benign	Het
Mindy4	T	C	6: 55,255,223 (GRCm39)	L567P	probably benign	Het
Mppe1	T	C	18: 67,370,472 (GRCm39)	D75G	probably damaging	Het
Muc4	C	T	16: 32,754,673 (GRCm38)	P1516S	probably benign	Het
Myo3b	C	A	2: 70,069,160 (GRCm39)	F494L	probably damaging	Het
Nedd4l	A	G	18: 65,298,688 (GRCm39)	T226A	probably benign	Het
Nod1	A	G	6: 54,921,277 (GRCm39)	V347A	probably benign	Het
Nup210	A	T	6: 91,019,235 (GRCm39)		probably null	Het
Nup210l	A	G	3: 90,025,932 (GRCm39)	R185G	probably damaging	Het
Oma1	T	C	4: 103,210,829 (GRCm39)	L445S	probably damaging	Het
Or13p10	A	T	4: 118,523,502 (GRCm39)	M263L	probably benign	Het
Or5ac20	A	T	16: 59,104,452 (GRCm39)	M136K	probably damaging	Het
Or8g36	A	G	9: 39,422,770 (GRCm39)	L82P	probably damaging	Het
Oxsm	A	T	14: 16,242,677 (GRCm38)	F31I	probably benign	Het
Pkd1l2	T	C	8: 117,740,615 (GRCm39)	T2161A	possibly damaging	Het
Pla2g3	A	T	11: 3,442,151 (GRCm39)	S404C	probably null	Het
Plec	A	G	15: 76,078,560 (GRCm39)	V60A	unknown	Het
Prpsap2	A	G	11: 61,643,736 (GRCm39)	S66P	possibly damaging	Het
Rarb	A	G	14: 16,436,804 (GRCm38)	L239P	probably damaging	Het
Ryr3	A	T	2: 112,583,395 (GRCm39)	Y2845*	probably null	Het
Spta1	T	C	1: 174,045,548 (GRCm39)	C1569R	probably damaging	Het
Stard13	G	A	5: 150,986,115 (GRCm39)	S465L	probably damaging	Het
Tmub1	A	T	5: 24,651,680 (GRCm39)	S80T	probably benign	Het
Trpv5	A	G	6: 41,647,847 (GRCm39)	F322S	probably damaging	Het
Vmn2r5	G	A	3: 64,411,203 (GRCm39)	A455V	probably benign	Het
Washc4	T	A	10: 83,405,882 (GRCm39)	N459K	probably damaging	Het
Wdr11	C	T	7: 129,207,437 (GRCm39)	R300*	probably null	Het
Zer1	A	G	2: 29,993,430 (GRCm39)	F559L	probably damaging	Het
Zfat	A	T	15: 68,052,519 (GRCm39)	V425D	probably damaging	Het
Zfp738	G	A	13: 67,817,910 (GRCm39)	L694F		Het
Zfp839	C	T	12: 110,835,277 (GRCm39)	A844V	probably damaging	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
IGL02954:Pdcd5	APN	7	35,343,089 (GRCm39)	missense	probably damaging	1.00
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
R9469:Pdcd5	UTSW	7	35,343,827 (GRCm39)	missense	probably benign	0.00

Predicted Primers

PCR Primer
(F):5'- GCAGCGAAAACCGAGACTTG -3'
(R):5'- GGCACTCGACTTTTGATGC -3'

Sequencing Primer
(F):5'- TGGGCACACACACGTTG -3'
(R):5'- GCACTCGACTTTTGATGCCTGAG -3'

Posted On

2021-08-02