Mutagenetix > Incidental Mutation

Incidental Mutation 'R1559:Smpdl3a'

170507

Institutional Source

Beutler Lab

Gene Symbol

Smpdl3a

Ensembl Gene

ENSMUSG00000019872

Gene Name

sphingomyelin phosphodiesterase, acid-like 3A

Synonyms

ASM3A, 0610010C24Rik, ASML3A

MMRRC Submission

039598-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R1559 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

57670640-57687926 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 57683588 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Threonine to Alanine at position 233 (T233A)

Ref Sequence

ENSEMBL: ENSMUSP00000020022 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000020022] [ENSMUST00000151623]

AlphaFold

P70158

Predicted Effect

probably damaging
Transcript: ENSMUST00000020022
AA Change: T233A

PolyPhen 2 Score 0.989 (Sensitivity: 0.72; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000020022
Gene: ENSMUSG00000019872
AA Change: T233A

Domain	Start	End	E-Value	Type
signal peptide	1	22	N/A	INTRINSIC
Pfam:Metallophos	35	294	1.7e-16	PFAM

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000125076

Predicted Effect

probably benign
Transcript: ENSMUST00000151623

Meta Mutation Damage Score

0.1493

Coding Region Coverage

1x: 98.8%
3x: 97.7%
10x: 94.0%
20x: 84.8%

Validation Efficiency

95% (73/77)

Allele List at MGI

Other mutations in this stock

Total: 60 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abca13	T	A	11: 9,349,180 (GRCm39)	W3585R	probably null	Het
Ajm1	G	T	2: 25,467,043 (GRCm39)	S956*	probably null	Het
Babam1	G	C	8: 71,850,424 (GRCm39)	E18Q	probably damaging	Het
Bcan	G	T	3: 87,901,519 (GRCm39)	S394R	probably damaging	Het
Birc6	T	A	17: 74,999,232 (GRCm39)	F4653L	probably damaging	Het
Camsap2	A	T	1: 136,209,832 (GRCm39)	H559Q	probably benign	Het
Cars2	G	T	8: 11,580,430 (GRCm39)		probably null	Het
Ccdc93	T	A	1: 121,389,712 (GRCm39)		probably benign	Het
Ccna2	C	A	3: 36,624,879 (GRCm39)		probably benign	Het
Cdc6	T	A	11: 98,803,037 (GRCm39)	L326I	probably damaging	Het
Cdh23	A	T	10: 60,255,478 (GRCm39)		probably benign	Het
Cenpe	T	A	3: 134,976,661 (GRCm39)	S2423T	probably benign	Het
Cftr	A	G	6: 18,225,936 (GRCm39)	M295V	probably benign	Het
Cxcl2	A	G	5: 91,051,871 (GRCm39)	H23R	probably benign	Het
Cyp4a12b	A	G	4: 115,291,181 (GRCm39)	T370A	probably damaging	Het
Daam2	A	G	17: 49,803,148 (GRCm39)		probably benign	Het
Dclk3	T	C	9: 111,298,276 (GRCm39)	F607L	probably damaging	Het
Des	T	G	1: 75,337,230 (GRCm39)	S57A	probably benign	Het
Drd1	A	T	13: 54,206,964 (GRCm39)	S410T	probably damaging	Het
Ecm1	G	A	3: 95,643,275 (GRCm39)	R342C	probably damaging	Het
Fanci	T	C	7: 79,082,941 (GRCm39)	L639P	probably damaging	Het
Fancm	A	G	12: 65,140,463 (GRCm39)	E395G	probably benign	Het
Grik3	A	G	4: 125,601,790 (GRCm39)	D889G	probably benign	Het
Heyl	A	G	4: 123,135,192 (GRCm39)	S62G	probably damaging	Het
Hmox1	C	T	8: 75,826,577 (GRCm39)	P267L	probably damaging	Het
Ifi213	A	C	1: 173,394,784 (GRCm39)	S584A	probably benign	Het
Il12rb2	G	T	6: 67,333,576 (GRCm39)	F234L	probably benign	Het
Il4i1	T	A	7: 44,488,811 (GRCm39)	S233T	probably damaging	Het
Itga4	A	G	2: 79,146,032 (GRCm39)	S745G	probably benign	Het
Kalrn	T	A	16: 33,830,918 (GRCm39)	I734F	possibly damaging	Het
Klk1b16	T	C	7: 43,790,425 (GRCm39)	I200T	probably benign	Het
Lrrc4c	T	A	2: 97,461,117 (GRCm39)	M581K	probably benign	Het
M6pr	A	T	6: 122,292,033 (GRCm39)	I122L	probably benign	Het
Magi3	T	C	3: 103,954,169 (GRCm39)		probably benign	Het
Mybpc2	T	G	7: 44,163,111 (GRCm39)	T480P	probably benign	Het
Or14c44	T	C	7: 86,061,575 (GRCm39)	S43P	probably benign	Het
Or1j17	A	G	2: 36,578,770 (GRCm39)	Y252C	probably damaging	Het
Or51ab3	A	T	7: 103,201,372 (GRCm39)	I127F	possibly damaging	Het
Or8g23	T	C	9: 38,971,437 (GRCm39)	N175S	probably benign	Het
Pcx	T	A	19: 4,669,114 (GRCm39)	I704N	probably damaging	Het
Pde3a	G	T	6: 141,404,824 (GRCm39)	A350S	probably damaging	Het
Ppox	A	T	1: 171,107,580 (GRCm39)		probably benign	Het
Prb1a	T	A	6: 132,185,507 (GRCm39)	Y42F	unknown	Het
Rsph4a	T	A	10: 33,785,727 (GRCm39)	V546E	probably damaging	Het
Saxo4	T	C	19: 10,458,770 (GRCm39)	T87A	probably benign	Het
Sf3b1	C	G	1: 55,058,554 (GRCm39)	E12Q	possibly damaging	Het
Sh3tc1	A	G	5: 35,860,693 (GRCm39)		probably null	Het
Slc22a2	T	C	17: 12,803,298 (GRCm39)	F44S	probably damaging	Het
Slco6c1	T	A	1: 97,026,223 (GRCm39)	D334V	probably damaging	Het
Smim19	T	C	8: 22,953,352 (GRCm39)	D105G	probably damaging	Het
St8sia5	G	A	18: 77,299,460 (GRCm39)		probably null	Het
Stk32a	C	A	18: 43,376,149 (GRCm39)	Q73K	probably benign	Het
Tmem129	G	T	5: 33,815,100 (GRCm39)		probably null	Het
Traf3ip3	A	T	1: 192,860,599 (GRCm39)	L441Q	probably damaging	Het
Ttn	C	T	2: 76,731,305 (GRCm39)		probably benign	Het
Unc45b	T	C	11: 82,808,672 (GRCm39)	S253P	possibly damaging	Het
Vars2	A	G	17: 35,977,150 (GRCm39)		probably benign	Het
Vmn2r51	C	T	7: 9,836,372 (GRCm39)	M136I	possibly damaging	Het
Vmn2r51	A	G	7: 9,836,373 (GRCm39)	M136T	possibly damaging	Het
Zfp595	T	C	13: 67,465,127 (GRCm39)	I379V	possibly damaging	Het

Other mutations in Smpdl3a

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00561:Smpdl3a	APN	10	57,684,042 (GRCm39)	missense	probably benign	0.01
IGL01530:Smpdl3a	APN	10	57,683,989 (GRCm39)	missense	probably damaging	1.00
IGL01936:Smpdl3a	APN	10	57,678,530 (GRCm39)	missense	probably damaging	1.00
IGL02342:Smpdl3a	APN	10	57,685,276 (GRCm39)	splice site	probably benign
IGL02372:Smpdl3a	APN	10	57,683,611 (GRCm39)	missense	probably benign	0.05
IGL02827:Smpdl3a	APN	10	57,678,592 (GRCm39)	missense	probably damaging	1.00
R0462:Smpdl3a	UTSW	10	57,670,827 (GRCm39)	missense	probably benign	0.07
R0658:Smpdl3a	UTSW	10	57,687,336 (GRCm39)	missense	probably damaging	0.99
R1216:Smpdl3a	UTSW	10	57,678,575 (GRCm39)	missense	probably null	0.98
R1502:Smpdl3a	UTSW	10	57,685,187 (GRCm39)	missense	probably damaging	1.00
R1807:Smpdl3a	UTSW	10	57,677,118 (GRCm39)	missense	probably damaging	0.99
R2872:Smpdl3a	UTSW	10	57,678,626 (GRCm39)	missense	possibly damaging	0.51
R2872:Smpdl3a	UTSW	10	57,678,626 (GRCm39)	missense	possibly damaging	0.51
R2877:Smpdl3a	UTSW	10	57,685,181 (GRCm39)	missense	probably damaging	1.00
R4799:Smpdl3a	UTSW	10	57,684,111 (GRCm39)	missense	probably damaging	1.00
R4814:Smpdl3a	UTSW	10	57,687,337 (GRCm39)	missense	probably damaging	1.00
R4916:Smpdl3a	UTSW	10	57,677,127 (GRCm39)	missense	probably damaging	1.00
R5137:Smpdl3a	UTSW	10	57,677,163 (GRCm39)	missense	possibly damaging	0.93
R5778:Smpdl3a	UTSW	10	57,677,097 (GRCm39)	missense	probably damaging	0.98
R5781:Smpdl3a	UTSW	10	57,684,034 (GRCm39)	missense	possibly damaging	0.78
R5917:Smpdl3a	UTSW	10	57,681,654 (GRCm39)	splice site	probably null
R6044:Smpdl3a	UTSW	10	57,687,358 (GRCm39)	missense	possibly damaging	0.82
R6773:Smpdl3a	UTSW	10	57,678,533 (GRCm39)	missense	probably damaging	0.99
R6863:Smpdl3a	UTSW	10	57,684,107 (GRCm39)	nonsense	probably null
R7480:Smpdl3a	UTSW	10	57,678,574 (GRCm39)	missense	possibly damaging	0.87
R7731:Smpdl3a	UTSW	10	57,678,650 (GRCm39)	missense	probably damaging	1.00
R7923:Smpdl3a	UTSW	10	57,677,141 (GRCm39)	missense	probably damaging	1.00
R8120:Smpdl3a	UTSW	10	57,683,547 (GRCm39)	missense	probably damaging	1.00
R8344:Smpdl3a	UTSW	10	57,677,073 (GRCm39)	missense	possibly damaging	0.81
R8377:Smpdl3a	UTSW	10	57,677,032 (GRCm39)	missense	possibly damaging	0.88
R8712:Smpdl3a	UTSW	10	57,687,526 (GRCm39)	missense	probably benign	0.44
R8876:Smpdl3a	UTSW	10	57,685,166 (GRCm39)	missense	probably damaging	1.00
R9003:Smpdl3a	UTSW	10	57,683,977 (GRCm39)	missense	probably damaging	1.00
R9145:Smpdl3a	UTSW	10	57,677,028 (GRCm39)	missense	possibly damaging	0.76
R9266:Smpdl3a	UTSW	10	57,678,596 (GRCm39)	missense	possibly damaging	0.51
Z1176:Smpdl3a	UTSW	10	57,681,714 (GRCm39)	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- AAGCAATGAGAACACCTGTCTACACTG -3'
(R):5'- TGGAACATGCGCTATGATGTATACCTG -3'

Sequencing Primer
(F):5'- AGAATTCACTTTCCCAAGTGTCTG -3'
(R):5'- CAGAGGACAACTTGTTTGCAC -3'

Posted On

2014-04-13