Mutagenetix > Incidental Mutation

Incidental Mutation 'PIT4431001:Gdpd3'

555240

Institutional Source

Beutler Lab

Gene Symbol

Gdpd3

Ensembl Gene

ENSMUSG00000030703

Gene Name

glycerophosphodiester phosphodiesterase domain containing 3

Synonyms

1110015E22Rik

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.069) question?

Stock #

PIT4431001 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

126365586-126374817 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 126365647 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Isoleucine to Threonine at position 2 (I2T)

Ref Sequence

ENSEMBL: ENSMUSP00000032944 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000032944] [ENSMUST00000050201] [ENSMUST00000057669] [ENSMUST00000091328]

AlphaFold

Q99LY2

Predicted Effect

probably benign
Transcript: ENSMUST00000032944
AA Change: I2T

PolyPhen 2 Score 0.055 (Sensitivity: 0.94; Specificity: 0.84)

SMART Domains

Protein: ENSMUSP00000032944
Gene: ENSMUSG00000030703
AA Change: I2T

Domain	Start	End	E-Value	Type
transmembrane domain	4	23	N/A	INTRINSIC
Pfam:GDPD	44	202	1.1e-23	PFAM
low complexity region	208	216	N/A	INTRINSIC
low complexity region	311	321	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000050201

SMART Domains

Protein: ENSMUSP00000101969
Gene: ENSMUSG00000063065

Domain	Start	End	E-Value	Type
low complexity region	2	32	N/A	INTRINSIC
S_TKc	43	331	3.3e-97	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000057669

SMART Domains

Protein: ENSMUSP00000051619
Gene: ENSMUSG00000063065

Domain	Start	End	E-Value	Type
low complexity region	2	32	N/A	INTRINSIC
S_TKc	43	331	3.3e-97	SMART
Blast:S_TKc	335	372	1e-15	BLAST

Predicted Effect

probably benign
Transcript: ENSMUST00000091328

SMART Domains

Protein: ENSMUSP00000088880
Gene: ENSMUSG00000063065

Domain	Start	End	E-Value	Type
Pfam:Pkinase_Tyr	1	213	2.5e-24	PFAM
Pfam:Pkinase	1	216	2.2e-58	PFAM
Pfam:APH	17	108	7.6e-7	PFAM
Blast:S_TKc	220	257	4e-16	BLAST

Predicted Effect

probably benign
Transcript: ENSMUST00000205657

Predicted Effect

probably benign
Transcript: ENSMUST00000206272

Coding Region Coverage

1x: 93.2%
3x: 90.7%
10x: 84.7%
20x: 71.4%

Validation Efficiency

MGI Phenotype

PHENOTYPE: Mice homozygous for an ENU-induced allele exhibit normal blood lymphocyte populations. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 74 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4930449I24Rik	A	G	5: 146,439,322 (GRCm39)	I29V	probably benign	Het
5730455P16Rik	C	A	11: 80,254,750 (GRCm39)	C357F	probably damaging	Het
Actr1a	A	T	19: 46,370,731 (GRCm39)		probably null	Het
Adcy1	C	G	11: 7,014,089 (GRCm39)	Q164E	possibly damaging	Het
Arhgap35	A	T	7: 16,295,536 (GRCm39)	S1176R	possibly damaging	Het
Atad2b	A	G	12: 5,081,795 (GRCm39)	T1235A	possibly damaging	Het
Atosb	C	A	4: 43,036,024 (GRCm39)	G236C	probably damaging	Het
Atp8a2	T	C	14: 59,892,075 (GRCm39)	D1091G	probably benign	Het
Bmp6	T	C	13: 38,669,906 (GRCm39)	S397P	probably benign	Het
C3	A	T	17: 57,513,242 (GRCm39)	N1468K	probably benign	Het
Ccnjl	CGCG	CGCGGCG	11: 43,470,534 (GRCm39)		probably benign	Het
Ccr1	T	C	9: 123,764,231 (GRCm39)	I100V	probably benign	Het
Cep162	T	A	9: 87,126,398 (GRCm39)	R171S	probably benign	Het
Chd8	T	C	14: 52,455,706 (GRCm39)	H994R	probably damaging	Het
Cntn3	T	A	6: 102,441,527 (GRCm39)	K6N	probably benign	Het
Cope	A	G	8: 70,765,417 (GRCm39)	E289G	probably damaging	Het
Cpne8	T	G	15: 90,436,178 (GRCm39)	E279A	probably damaging	Het
Cyp11a1	A	T	9: 57,923,555 (GRCm39)		probably null	Het
Dcp2	A	G	18: 44,545,638 (GRCm39)	K333R	probably benign	Het
Dpp6	G	T	5: 27,836,496 (GRCm39)	V329F	probably benign	Het
Drc1	T	A	5: 30,504,417 (GRCm39)	D186E	probably damaging	Het
Dsc2	G	A	18: 20,179,334 (GRCm39)	Q245*	probably null	Het
Eef1e1	T	C	13: 38,842,938 (GRCm39)	E11G	probably damaging	Het
Emilin2	G	A	17: 71,562,990 (GRCm39)	P915S	probably benign	Het
Fpgt	A	G	3: 154,792,422 (GRCm39)	M535T	possibly damaging	Het
Fxyd3	G	A	7: 30,770,780 (GRCm39)	L37F	probably damaging	Het
Gal3st2c	T	A	1: 93,935,834 (GRCm39)	I62N	probably damaging	Het
Gm9611	T	C	14: 42,115,888 (GRCm39)	M169V		Het
Ints3	G	A	3: 90,303,767 (GRCm39)	T720I	probably damaging	Het
Itpr2	T	G	6: 146,256,218 (GRCm39)	M992L	probably benign	Het
L3mbtl2	T	A	15: 81,560,508 (GRCm39)	H256Q	probably benign	Het
Lama2	T	C	10: 26,977,426 (GRCm39)	T1918A	probably damaging	Het
Lpcat2b	G	A	5: 107,581,997 (GRCm39)	G442D	probably damaging	Het
Lrp1b	C	T	2: 40,894,767 (GRCm39)	V2268M		Het
Macc1	T	C	12: 119,410,246 (GRCm39)	L338P	probably benign	Het
Mtmr2	T	C	9: 13,704,475 (GRCm39)	F201L	probably benign	Het
Mtr	C	T	13: 12,227,329 (GRCm39)	V772M	probably damaging	Het
Mtus2	A	G	5: 148,013,515 (GRCm39)	T103A	probably benign	Het
Myo5c	A	G	9: 75,159,853 (GRCm39)	I294V	possibly damaging	Het
Ncam1	A	T	9: 49,709,993 (GRCm39)	F13I	probably benign	Het
Or4a75	T	C	2: 89,448,201 (GRCm39)	I112V	probably benign	Het
Paqr6	A	T	3: 88,273,084 (GRCm39)	I52F	possibly damaging	Het
Pde2a	T	G	7: 101,151,104 (GRCm39)	V271G	probably damaging	Het
Pde7b	T	C	10: 20,276,291 (GRCm39)	H405R	possibly damaging	Het
Plxnb1	A	G	9: 108,929,786 (GRCm39)	Y214C	probably damaging	Het
Pmp22	T	C	11: 63,042,067 (GRCm39)	F101L	probably benign	Het
Pold1	A	G	7: 44,188,318 (GRCm39)	L520P	probably damaging	Het
Pramel1	A	G	4: 143,124,960 (GRCm39)	T295A	possibly damaging	Het
Psg20	A	T	7: 18,408,475 (GRCm39)	I415N	probably damaging	Het
Ptcd2	T	A	13: 99,476,527 (GRCm39)	R71*	probably null	Het
Ptgs1	A	T	2: 36,130,692 (GRCm39)	N197I	probably damaging	Het
Rbfox3	T	C	11: 118,386,047 (GRCm39)	D333G	probably damaging	Het
Rfx7	T	A	9: 72,525,253 (GRCm39)	H814Q	probably benign	Het
Rptn	TGGGTCAGAAAGGCAGGCATGACCAGAGTCCTCACCAGGGTCAGAAAGGCAGGCATGACCAGAGTCCTCACCAGGGTCAGAAAGGCAGACAAGACCTGAGTTCTCACCAGGGTCAGAAAGGCAGACAAGACCAGAGTCCTCACCTGGGTCAGAAAGGCAGGCATGACCAGAGTCCTCACCGGGGTCAGAAAGGCAGGCAAGACCAGAGTCCTCACCAGGGTCAGAAAGGCAG	TGGGTCAGAAAGGCAGGCATGACCAGAGTCCTCACCAGGGTCAGAAAGGCAGACAAGACCTGAGTTCTCACCAGGGTCAGAAAGGCAGACAAGACCAGAGTCCTCACCTGGGTCAGAAAGGCAGGCATGACCAGAGTCCTCACCGGGGTCAGAAAGGCAGGCAAGACCAGAGTCCTCACCAGGGTCAGAAAGGCAG	3: 93,304,704 (GRCm39)		probably benign	Het
Serpina3i	A	T	12: 104,231,432 (GRCm39)	H23L	probably benign	Het
Sipa1l1	T	A	12: 82,443,290 (GRCm39)	V860E	probably benign	Het
Slc12a1	T	A	2: 125,032,124 (GRCm39)	Y592N	possibly damaging	Het
Slco2a1	T	C	9: 102,927,467 (GRCm39)	F120S	probably damaging	Het
Smyd4	T	C	11: 75,294,339 (GRCm39)	F740S	probably damaging	Het
Sppl2a	T	C	2: 126,765,396 (GRCm39)	Y242C	probably damaging	Het
Sqle	A	G	15: 59,195,509 (GRCm39)	K288R	probably benign	Het
Tbc1d17	A	G	7: 44,494,498 (GRCm39)	S246P	probably benign	Het
Tenm3	G	A	8: 48,688,642 (GRCm39)	T2315M	probably damaging	Het
Tgfb1i1	C	T	7: 127,848,353 (GRCm39)	R191C	probably damaging	Het
Thumpd3	T	A	6: 113,036,939 (GRCm39)	N279K	probably benign	Het
Tmed5	T	A	5: 108,277,887 (GRCm39)	H95L	possibly damaging	Het
Tmem161a	T	C	8: 70,634,674 (GRCm39)	L443P	probably damaging	Het
Ttc38	C	A	15: 85,720,328 (GRCm39)	Q97K	probably benign	Het
Unc13c	C	A	9: 73,656,829 (GRCm39)	C1124F	probably damaging	Het
Vmn2r102	A	G	17: 19,896,958 (GRCm39)	T102A	possibly damaging	Het
Vwce	G	A	19: 10,641,946 (GRCm39)	E891K	possibly damaging	Het
Xkr5	A	T	8: 18,984,361 (GRCm39)	S394T	possibly damaging	Het
Zan	C	T	5: 137,390,326 (GRCm39)	C4747Y	unknown	Het
Zfp804a	T	C	2: 82,089,536 (GRCm39)	F1122L	probably benign	Het

Other mutations in Gdpd3

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00753:Gdpd3	APN	7	126,366,598 (GRCm39)	nonsense	probably null
IGL01113:Gdpd3	APN	7	126,366,997 (GRCm39)	missense	probably benign	0.01
IGL01433:Gdpd3	APN	7	126,370,356 (GRCm39)	missense	possibly damaging	0.82
IGL01465:Gdpd3	APN	7	126,367,829 (GRCm39)	missense	possibly damaging	0.63
IGL01736:Gdpd3	APN	7	126,365,695 (GRCm39)	missense	probably damaging	0.99
R0118:Gdpd3	UTSW	7	126,370,165 (GRCm39)	missense	probably damaging	1.00
R0311:Gdpd3	UTSW	7	126,366,361 (GRCm39)	missense	possibly damaging	0.79
R2049:Gdpd3	UTSW	7	126,367,766 (GRCm39)	missense	probably damaging	0.99
R4976:Gdpd3	UTSW	7	126,366,454 (GRCm39)	missense	probably damaging	1.00
R6151:Gdpd3	UTSW	7	126,374,674 (GRCm39)	missense	probably benign	0.00
R6170:Gdpd3	UTSW	7	126,370,336 (GRCm39)	missense	probably benign	0.04
R6898:Gdpd3	UTSW	7	126,370,201 (GRCm39)	nonsense	probably null
R8236:Gdpd3	UTSW	7	126,367,838 (GRCm39)	missense	probably benign	0.26

Predicted Primers

PCR Primer
(F):5'- AAGGTCTCTGGACATGGAACC -3'
(R):5'- ATGGATTCCAGCCCTTCCAC -3'

Sequencing Primer
(F):5'- TCTGGGCCATACTGCAGTCTG -3'
(R):5'- ACCTCCCTGACTCAGCTCAC -3'

Posted On

2019-06-07