Mutagenetix > Incidental Mutation

Incidental Mutation 'R7394:Smpd3'

573667

Institutional Source

Beutler Lab

Gene Symbol

Smpd3

Ensembl Gene

ENSMUSG00000031906

Gene Name

sphingomyelin phosphodiesterase 3, neutral

Synonyms

4631433G07Rik, neutral sphingomyelinase II, nSMase2, fro, Nsm2

MMRRC Submission

045476-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.904) question?

Stock #

R7394 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

106979180-107064597 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

G to A at 106991642 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Arginine to Tryptophan at position 304 (R304W)

Ref Sequence

ENSEMBL: ENSMUSP00000069255 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000067512] [ENSMUST00000212896]

AlphaFold

Q9JJY3

Predicted Effect

probably damaging
Transcript: ENSMUST00000067512
AA Change: R304W

PolyPhen 2 Score 0.991 (Sensitivity: 0.71; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000069255
Gene: ENSMUSG00000031906
AA Change: R304W

Domain	Start	End	E-Value	Type
transmembrane domain	15	37	N/A	INTRINSIC
transmembrane domain	57	79	N/A	INTRINSIC
low complexity region	178	189	N/A	INTRINSIC
Pfam:Exo_endo_phos	321	639	1.2e-15	PFAM

Predicted Effect

probably damaging
Transcript: ENSMUST00000212896
AA Change: R304W

PolyPhen 2 Score 0.991 (Sensitivity: 0.71; Specificity: 0.97)

Coding Region Coverage

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

Validation Efficiency

99% (66/67)

MGI Phenotype

PHENOTYPE: Homozygous null mice exhibit dwarfism, delayed sexual and gonad maturation, delayed ossification of the long bones, and reduced serum levels of thyroxine, triiodothyronine, cortisol, and insulin-like growth factor. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 69 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1700017N19Rik	A	G	10: 100,445,038 (GRCm39)	I208V	probably benign	Het
Abcb11	C	T	2: 69,130,211 (GRCm39)	D282N	probably damaging	Het
Aldh1l2	T	A	10: 83,338,321 (GRCm39)	I646F	probably damaging	Het
Alms1	C	T	6: 85,599,205 (GRCm39)	P1344S	possibly damaging	Het
Ank2	T	A	3: 126,730,302 (GRCm39)	I711L	possibly damaging	Het
Ankrd6	T	C	4: 32,821,298 (GRCm39)	N251D	probably damaging	Het
Ap3m1	T	C	14: 21,088,147 (GRCm39)	T304A	probably benign	Het
Arhgef39	T	C	4: 43,499,532 (GRCm39)	T26A	possibly damaging	Het
Carnmt1	G	T	19: 18,648,201 (GRCm39)		probably benign	Het
Ccr4	C	T	9: 114,320,994 (GRCm39)	R357H	probably benign	Het
Cd4	T	A	6: 124,850,004 (GRCm39)	M104L	probably benign	Het
Cd74	A	T	18: 60,936,965 (GRCm39)		probably benign	Het
Cdcp1	T	C	9: 123,002,878 (GRCm39)	Y731C	probably damaging	Het
Cdyl2	A	G	8: 117,350,790 (GRCm39)	S114P	not run	Het
Cenpv	T	C	11: 62,427,114 (GRCm39)	D148G	probably damaging	Het
Cep89	G	A	7: 35,129,353 (GRCm39)	R630H	probably damaging	Het
Cfap57	T	A	4: 118,450,334 (GRCm39)	Y596F	probably benign	Het
Clec4a2	C	A	6: 123,116,079 (GRCm39)	A122E	unknown	Het
Col4a2	A	G	8: 11,496,184 (GRCm39)	T1602A	probably benign	Het
Cracd	GCGCGAGGCCGAGAGGCAGGAGGAGGAAGCAAGACAACGCGAGGCCGAGAGGCAGG	GCGCGAGGCCGAGAGGCAGG	5: 77,004,801 (GRCm39)		probably benign	Het
Cyp2j11	A	T	4: 96,204,677 (GRCm39)	Y290N	probably benign	Het
Dhx38	A	T	8: 110,283,155 (GRCm39)	V554E	probably damaging	Het
Ebf2	T	C	14: 67,474,975 (GRCm39)	V70A	probably damaging	Het
Enpp5	G	A	17: 44,396,155 (GRCm39)	G356S	probably damaging	Het
Fam217a	A	T	13: 35,094,262 (GRCm39)	I499K	possibly damaging	Het
Fras1	C	A	5: 96,860,309 (GRCm39)	Y2118*	probably null	Het
Gm3248	A	T	14: 5,945,781 (GRCm38)		probably null	Het
Gm5460	T	G	14: 33,765,879 (GRCm39)	D165E	possibly damaging	Het
Grk4	A	T	5: 34,908,962 (GRCm39)	N490Y	probably benign	Het
Iglc2	T	A	16: 19,013,886 (GRCm39)	K59*	probably null	Het
Iqsec3	T	A	6: 121,363,569 (GRCm39)	H895L	possibly damaging	Het
Itgb7	A	G	15: 102,127,689 (GRCm39)	S410P	probably damaging	Het
Kmt2d	C	A	15: 98,754,265 (GRCm39)	V1613F	unknown	Het
Lama1	T	C	17: 68,024,256 (GRCm39)	L118P		Het
Lrrc25	A	T	8: 71,070,830 (GRCm39)	S204C	possibly damaging	Het
Malrd1	A	G	2: 15,700,010 (GRCm39)	D619G	unknown	Het
Ms4a6d	G	A	19: 11,567,437 (GRCm39)	Q155*	probably null	Het
Mup17	G	A	4: 61,512,635 (GRCm39)	S86F	probably benign	Het
Nbeal2	C	T	9: 110,459,257 (GRCm39)		probably null	Het
Nfkb1	A	C	3: 135,319,458 (GRCm39)	V291G	possibly damaging	Het
Nomo1	G	T	7: 45,715,903 (GRCm39)	V757F	probably benign	Het
Nutm2	T	A	13: 50,624,043 (GRCm39)	S247T	probably damaging	Het
Or2at1	C	A	7: 99,416,553 (GRCm39)	H61Q	probably damaging	Het
Or4c120	C	T	2: 89,000,705 (GRCm39)	V284I	probably benign	Het
Or4f4-ps1	G	T	2: 111,330,241 (GRCm39)	A215S	probably damaging	Het
Or7g12	T	A	9: 18,900,006 (GRCm39)	C241S	probably damaging	Het
Or9k2b	T	A	10: 130,016,123 (GRCm39)	I209F	probably damaging	Het
Pcdhb14	A	G	18: 37,581,961 (GRCm39)	I356V	probably benign	Het
Pnkp	T	A	7: 44,508,102 (GRCm39)	S142T	probably damaging	Het
Ppia	T	C	11: 6,369,218 (GRCm39)	S99P	possibly damaging	Het
Prss47	C	T	13: 65,192,807 (GRCm39)	V325I	probably benign	Het
Ptgr3	C	T	18: 84,106,315 (GRCm39)	A9V	probably benign	Het
Ptk7	T	C	17: 46,902,683 (GRCm39)	D34G	probably damaging	Het
Pwp2	C	T	10: 78,018,314 (GRCm39)	G126R	probably damaging	Het
Rasa3	G	T	8: 13,645,353 (GRCm39)	D195E	probably benign	Het
Rnf150	T	A	8: 83,717,100 (GRCm39)	Y202*	probably null	Het
Sh2d1b2	T	C	1: 170,075,716 (GRCm39)	V50A	probably damaging	Het
Slc30a4	C	T	2: 122,527,224 (GRCm39)	V390I	possibly damaging	Het
Slc30a9	G	T	5: 67,510,109 (GRCm39)		probably null	Het
Slc8a3	T	A	12: 81,260,832 (GRCm39)		probably null	Het
Snta1	A	G	2: 154,218,780 (GRCm39)	S490P	probably damaging	Het
Srcap	T	G	7: 127,134,000 (GRCm39)	M887R	probably damaging	Het
St3gal1	A	G	15: 66,983,195 (GRCm39)	V187A	possibly damaging	Het
Sult2a3	T	C	7: 13,845,449 (GRCm39)	T137A	probably benign	Het
Tspoap1	C	T	11: 87,656,945 (GRCm39)	Q367*	probably null	Het
Uroc1	C	T	6: 90,322,315 (GRCm39)	R280C	probably damaging	Het
Ush2a	T	C	1: 188,643,613 (GRCm39)	I4325T	possibly damaging	Het
Vmn1r32	A	G	6: 66,530,173 (GRCm39)	I201T	probably benign	Het
Zbtb47	T	A	9: 121,596,411 (GRCm39)	M626K	probably damaging	Het

Other mutations in Smpd3

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL03380:Smpd3	APN	8	106,986,291 (GRCm39)	missense	probably benign	0.01
BB010:Smpd3	UTSW	8	106,982,254 (GRCm39)	missense	probably benign
BB020:Smpd3	UTSW	8	106,982,254 (GRCm39)	missense	probably benign
G1citation:Smpd3	UTSW	8	106,992,596 (GRCm39)	start gained	probably benign
R0240:Smpd3	UTSW	8	106,991,788 (GRCm39)	missense	probably damaging	0.96
R0240:Smpd3	UTSW	8	106,991,788 (GRCm39)	missense	probably damaging	0.96
R0456:Smpd3	UTSW	8	106,986,288 (GRCm39)	missense	probably benign
R0759:Smpd3	UTSW	8	106,991,860 (GRCm39)	missense	probably benign	0.34
R0799:Smpd3	UTSW	8	106,991,421 (GRCm39)	missense	possibly damaging	0.92
R1544:Smpd3	UTSW	8	106,992,199 (GRCm39)	missense	possibly damaging	0.70
R1756:Smpd3	UTSW	8	106,991,603 (GRCm39)	missense	probably benign
R2937:Smpd3	UTSW	8	106,991,452 (GRCm39)	missense	probably damaging	1.00
R2939:Smpd3	UTSW	8	106,984,039 (GRCm39)	missense	probably benign	0.00
R4614:Smpd3	UTSW	8	106,986,371 (GRCm39)	missense	probably damaging	1.00
R5829:Smpd3	UTSW	8	106,991,512 (GRCm39)	missense	probably benign	0.15
R6822:Smpd3	UTSW	8	106,992,596 (GRCm39)	start gained	probably benign
R6891:Smpd3	UTSW	8	106,991,300 (GRCm39)	missense	probably damaging	1.00
R6962:Smpd3	UTSW	8	106,991,851 (GRCm39)	missense	probably benign	0.34
R6965:Smpd3	UTSW	8	106,986,513 (GRCm39)	missense	probably damaging	1.00
R7344:Smpd3	UTSW	8	106,991,825 (GRCm39)	missense	probably damaging	1.00
R7823:Smpd3	UTSW	8	106,982,254 (GRCm39)	missense	probably benign
R7825:Smpd3	UTSW	8	106,982,254 (GRCm39)	missense	probably benign
R7933:Smpd3	UTSW	8	106,982,254 (GRCm39)	missense	probably benign
R7974:Smpd3	UTSW	8	106,982,254 (GRCm39)	missense	probably benign
R7975:Smpd3	UTSW	8	106,982,254 (GRCm39)	missense	probably benign
R7976:Smpd3	UTSW	8	106,982,254 (GRCm39)	missense	probably benign
R7977:Smpd3	UTSW	8	106,986,526 (GRCm39)	missense	probably benign	0.11
R7987:Smpd3	UTSW	8	106,986,526 (GRCm39)	missense	probably benign	0.11
R8260:Smpd3	UTSW	8	106,984,047 (GRCm39)	missense	probably benign	0.13
R8264:Smpd3	UTSW	8	106,991,290 (GRCm39)	missense	probably damaging	1.00
R8292:Smpd3	UTSW	8	106,991,422 (GRCm39)	missense	probably benign	0.08
R8432:Smpd3	UTSW	8	106,984,309 (GRCm39)	critical splice acceptor site	probably null
R8494:Smpd3	UTSW	8	106,981,982 (GRCm39)	missense	probably damaging	0.99
R8779:Smpd3	UTSW	8	106,992,121 (GRCm39)	missense	probably benign	0.37
R8787:Smpd3	UTSW	8	106,982,377 (GRCm39)	missense	probably damaging	1.00
R9005:Smpd3	UTSW	8	106,984,058 (GRCm39)	missense	probably benign	0.02
R9008:Smpd3	UTSW	8	106,984,058 (GRCm39)	missense	probably benign	0.02
R9355:Smpd3	UTSW	8	106,991,825 (GRCm39)	missense	probably damaging	1.00
R9516:Smpd3	UTSW	8	106,992,119 (GRCm39)	missense	probably benign	0.03
R9698:Smpd3	UTSW	8	106,992,296 (GRCm39)	missense	possibly damaging	0.54
R9703:Smpd3	UTSW	8	106,991,713 (GRCm39)	missense	probably damaging	0.99
Z1177:Smpd3	UTSW	8	106,991,474 (GRCm39)	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- TTCAACTTAGCAGCCGCACG -3'
(R):5'- TGAGGACAGCTGCATTGTG -3'

Sequencing Primer
(F):5'- GCTTGTCAAACACCTCCTGCAG -3'
(R):5'- CATTGTGCGAATTGGTGGC -3'

Posted On

2019-09-13