Mutagenetix > Incidental Mutation

Incidental Mutation 'R9469:Pdcd5'

715353

Institutional Source

Beutler Lab

Gene Symbol

Pdcd5

Ensembl Gene

ENSMUSG00000030417

Gene Name

programmed cell death 5

Synonyms

2200003D22Rik, Tfar19

MMRRC Submission

Accession Numbers

Essential gene?

Probably essential (E-score: 0.960) question?

Stock #

R9469 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

35341410-35346907 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 35343827 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Methionine to Valine at position 39 (M39V)

Ref Sequence

ENSEMBL: ENSMUSP00000113761 (fasta)

Gene Model

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

AlphaFold

P56812

Predicted Effect

probably benign
Transcript: ENSMUST00000118501
AA Change: M39V

PolyPhen 2 Score 0.003 (Sensitivity: 0.98; Specificity: 0.44)

SMART Domains

Protein: ENSMUSP00000113761
Gene: ENSMUSG00000030417
AA Change: M39V

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

Predicted Effect

probably benign
Transcript: ENSMUST00000120714
AA Change: M118V

PolyPhen 2 Score 0.091 (Sensitivity: 0.93; Specificity: 0.85)

SMART Domains

Protein: ENSMUSP00000113013
Gene: ENSMUSG00000030417
AA Change: M118V

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: 99.5%
20x: 98.2%

Validation Efficiency

Allele List at MGI

Other mutations in this stock

Total: 78 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Acsbg3	A	T	17: 57,183,283 (GRCm39)	D8V	probably benign	Het
Ada	T	A	2: 163,574,192 (GRCm39)	M155L	probably benign	Het
Adam23	A	G	1: 63,584,671 (GRCm39)	I360V	probably benign	Het
Ahnak	G	A	19: 8,988,225 (GRCm39)	G3170R	probably damaging	Het
Alb	G	A	5: 90,610,659 (GRCm39)	D80N	probably benign	Het
Amph	G	T	13: 19,270,769 (GRCm39)	G126V	probably damaging	Het
Anks1b	A	T	10: 90,733,205 (GRCm39)	M994L	possibly damaging	Het
Atp8a2	A	G	14: 60,028,668 (GRCm39)	L933P	probably benign	Het
Bcas1	T	C	2: 170,191,292 (GRCm39)	D546G	possibly damaging	Het
Bmpr2	A	C	1: 59,881,928 (GRCm39)	M186L	probably benign	Het
Clca3a2	T	C	3: 144,507,938 (GRCm39)	I711V	probably damaging	Het
Cobll1	G	A	2: 64,966,774 (GRCm39)	T128I	probably damaging	Het
Cog4	T	C	8: 111,608,804 (GRCm39)	W165R	unknown	Het
Cyp2j5	G	A	4: 96,517,731 (GRCm39)	R494*	probably null	Het
Dnah2	G	A	11: 69,321,896 (GRCm39)	A3808V	probably damaging	Het
Dnah5	A	T	15: 28,421,146 (GRCm39)	T3828S	probably benign	Het
Dsg1c	T	C	18: 20,400,947 (GRCm39)	I150T	probably damaging	Het
Ehd2	A	T	7: 15,684,332 (GRCm39)	I489N	probably damaging	Het
Fam24a	C	A	7: 130,938,392 (GRCm39)	T94K	probably damaging	Het
Gata2	A	G	6: 88,182,301 (GRCm39)	E423G	possibly damaging	Het
Gm8947	A	G	1: 151,069,063 (GRCm39)	I299V	unknown	Het
Gpr161	A	G	1: 165,133,896 (GRCm39)	I53V	possibly damaging	Het
Guca2b	G	A	4: 119,515,817 (GRCm39)	Q15*	probably null	Het
Hus1	A	G	11: 8,948,744 (GRCm39)	V219A	probably benign	Het
Il5	T	C	11: 53,614,824 (GRCm39)	W129R	probably damaging	Het
Ipmk	A	G	10: 71,201,843 (GRCm39)	Y77C	probably damaging	Het
Kcnip3	A	G	2: 127,307,322 (GRCm39)	L136P	probably benign	Het
Klhl2	G	A	8: 65,196,069 (GRCm39)	A558V	probably benign	Het
Klra5	C	A	6: 129,883,686 (GRCm39)	W147L	possibly damaging	Het
Lig3	G	A	11: 82,686,199 (GRCm39)	C613Y	probably benign	Het
Lrriq1	A	G	10: 103,050,761 (GRCm39)	S664P	probably benign	Het
Megf6	A	G	4: 154,335,369 (GRCm39)	Y276C	probably damaging	Het
Mlph	A	G	1: 90,856,068 (GRCm39)	E119G	probably damaging	Het
Mrpl39	T	G	16: 84,517,170 (GRCm39)	R316S	probably damaging	Het
Myo18b	T	C	5: 112,994,247 (GRCm39)	D902G	probably benign	Het
Myocd	A	G	11: 65,087,220 (GRCm39)	S236P	probably benign	Het
Myom1	G	T	17: 71,368,122 (GRCm39)	A482S	possibly damaging	Het
Nol4	A	G	18: 23,085,318 (GRCm39)	V32A	probably damaging	Het
Nrp2	T	C	1: 62,804,030 (GRCm39)	Y555H	probably damaging	Het
Or12d12	T	C	17: 37,610,956 (GRCm39)	D119G	probably damaging	Het
Or4d10c	G	A	19: 12,065,434 (GRCm39)	H241Y	probably benign	Het
Or52l1	A	T	7: 104,829,967 (GRCm39)	H199Q	probably damaging	Het
Or8k27	C	A	2: 86,275,787 (GRCm39)	D180Y	probably damaging	Het
Papss1	A	G	3: 131,288,959 (GRCm39)	K175E	possibly damaging	Het
Plcl2	G	A	17: 50,913,953 (GRCm39)	D321N	probably benign	Het
Plxna4	G	A	6: 32,494,526 (GRCm39)	P30L	probably benign	Het
Pou2f1	G	A	1: 165,740,830 (GRCm39)	T113I	probably benign	Het
Ptpn2	T	A	18: 67,808,907 (GRCm39)	H303L	probably benign	Het
R3hdm1	T	A	1: 128,106,921 (GRCm39)		probably null	Het
Rdx	T	C	9: 51,977,069 (GRCm39)	V106A	probably damaging	Het
Ripk2	T	C	4: 16,138,181 (GRCm39)	D249G	possibly damaging	Het
Rnf169	A	T	7: 99,575,567 (GRCm39)	S343T	possibly damaging	Het
Rnf40	T	A	7: 127,195,769 (GRCm39)	L671Q	probably damaging	Het
Scube3	C	A	17: 28,386,138 (GRCm39)	S793*	probably null	Het
Sipa1l3	A	T	7: 29,028,481 (GRCm39)	M1633K	possibly damaging	Het
Slc16a14	A	T	1: 84,900,612 (GRCm39)	N124K	probably benign	Het
Smarcd2	G	A	11: 106,163,332 (GRCm39)	A68V	probably benign	Het
Smg1	T	C	7: 117,739,774 (GRCm39)	E3391G	possibly damaging	Het
Spata32	T	C	11: 103,099,741 (GRCm39)	M255V	possibly damaging	Het
Sstr5	T	A	17: 25,710,941 (GRCm39)	Q96L	probably damaging	Het
Tcaf3	A	G	6: 42,573,828 (GRCm39)	I128T	probably benign	Het
Tfdp1	C	T	8: 13,422,965 (GRCm39)	T290M	probably benign	Het
Ticrr	C	T	7: 79,344,511 (GRCm39)	H1459Y	probably benign	Het
Tmed4	T	A	11: 6,223,763 (GRCm39)	Q171L	probably benign	Het
Tmem40	G	A	6: 115,719,321 (GRCm39)	S48F	possibly damaging	Het
Tnfaip1	A	G	11: 78,419,075 (GRCm39)		probably null	Het
Top1mt	A	G	15: 75,539,742 (GRCm39)	Y290H	probably damaging	Het
Topaz1	A	T	9: 122,577,585 (GRCm39)	D165V	probably damaging	Het
Trim44	T	C	2: 102,230,651 (GRCm39)	S127G	unknown	Het
Ubac1	G	A	2: 25,897,763 (GRCm39)	R286C	probably damaging	Het
Ube2u	A	G	4: 100,406,958 (GRCm39)	E273G	possibly damaging	Het
Vmn1r213	G	A	13: 23,196,101 (GRCm39)	S228N	probably benign	Het
Vmn2r28	A	T	7: 5,487,118 (GRCm39)	V515E	probably damaging	Het
Vps13d	A	G	4: 144,780,691 (GRCm39)	L4011P		Het
Ythdc2	T	C	18: 45,019,383 (GRCm39)	F1384S	probably damaging	Het
Zfp423	T	A	8: 88,509,519 (GRCm39)	Y275F	probably damaging	Het
Zfp493	A	G	13: 67,934,325 (GRCm39)	K93E	probably benign	Het
Zfp980	G	T	4: 145,427,687 (GRCm39)	G139W	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
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
R8896:Pdcd5	UTSW	7	35,346,795 (GRCm39)	start codon destroyed	probably null	0.84

Predicted Primers

PCR Primer
(F):5'- TGTTCAAGAGTCAATCCCTCC -3'
(R):5'- CCATGCAGTCGGAACTAGAG -3'

Sequencing Primer
(F):5'- AGAGTCAATCCCTCCAAACTTTTCTG -3'
(R):5'- TCATGATCTGAGGTCAAGCTTC -3'

Posted On

2022-06-15