Mutagenetix > Incidental Mutation

Incidental Mutation 'R7976:Smpd3'

650916

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

046019-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.922) question?

Stock #

R7976 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

106979180-107064597 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to C at 106982254 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Cysteine to Glycine at position 617 (C617G)

Ref Sequence

ENSEMBL: ENSMUSP00000148282 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000067512] [ENSMUST00000071592] [ENSMUST00000212896]

AlphaFold

Q9JJY3

Predicted Effect

probably benign
Transcript: ENSMUST00000067512
AA Change: C617G

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)

SMART Domains

Protein: ENSMUSP00000069255
Gene: ENSMUSG00000031906
AA Change: C617G

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 benign
Transcript: ENSMUST00000071592

SMART Domains

Protein: ENSMUSP00000071521
Gene: ENSMUSG00000060098

Domain	Start	End	E-Value	Type
Pfam:PrmA	53	148	1.6e-7	PFAM
internal_repeat_1	382	652	1.71e-8	PROSPERO

Predicted Effect

probably benign
Transcript: ENSMUST00000212896
AA Change: C617G

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)

Coding Region Coverage

1x: 100.0%
3x: 100.0%
10x: 99.8%
20x: 99.2%

Validation Efficiency

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: 70 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Adss1	A	C	12: 112,602,831 (GRCm39)	I341L	probably benign	Het
Aldh1b1	T	A	4: 45,803,092 (GRCm39)	M210K	possibly damaging	Het
Ankrd17	G	A	5: 90,431,451 (GRCm39)	Q778*	probably null	Het
Bmper	T	C	9: 23,318,106 (GRCm39)	V575A	probably damaging	Het
Brinp2	A	G	1: 158,073,913 (GRCm39)	V736A	probably benign	Het
Ccdc81	A	T	7: 89,515,723 (GRCm39)	L652*	probably null	Het
Cdt1	C	T	8: 123,298,585 (GRCm39)	R437W	probably damaging	Het
Ckb	A	C	12: 111,637,466 (GRCm39)	L165R	possibly damaging	Het
Col25a1	G	T	3: 130,290,075 (GRCm39)	G255V	probably damaging	Het
Ddx17	A	G	15: 79,420,156 (GRCm39)		probably null	Het
Dennd4a	G	T	9: 64,759,794 (GRCm39)	G300W	possibly damaging	Het
Dlg4	T	A	11: 69,930,008 (GRCm39)	I316N	probably damaging	Het
Dlgap2	C	T	8: 14,793,410 (GRCm39)	P467L	probably benign	Het
Dnah9	T	C	11: 65,732,227 (GRCm39)	I4226M	possibly damaging	Het
Drc1	G	A	5: 30,521,829 (GRCm39)	A734T	probably benign	Het
Entpd1	A	G	19: 40,600,865 (GRCm39)	M1V	probably null	Het
Exph5	T	G	9: 53,287,935 (GRCm39)	I1672S	possibly damaging	Het
Fam149b	T	A	14: 20,427,852 (GRCm39)	D379E	probably damaging	Het
Fgfr2	T	C	7: 129,787,074 (GRCm39)	T461A	probably damaging	Het
Frem1	A	G	4: 82,919,946 (GRCm39)	V469A	probably damaging	Het
Frem3	A	T	8: 81,338,231 (GRCm39)	K175*	probably null	Het
Fsd2	C	T	7: 81,209,629 (GRCm39)	G71E	probably benign	Het
Gcat	T	C	15: 78,919,188 (GRCm39)	I116T	probably damaging	Het
Gigyf2	G	A	1: 87,331,458 (GRCm39)	S202N	unknown	Het
Glra3	T	G	8: 56,565,911 (GRCm39)		probably null	Het
Golga4	C	T	9: 118,365,836 (GRCm39)	T296I	possibly damaging	Het
Herc1	C	T	9: 66,341,552 (GRCm39)	T1816I	possibly damaging	Het
Igfbpl1	C	A	4: 45,826,786 (GRCm39)	R3L	unknown	Het
Ighv15-2	A	T	12: 114,528,470 (GRCm39)	S28T	probably benign	Het
Kat2b	T	A	17: 53,955,835 (GRCm39)	M427K	probably benign	Het
Kdm4c	A	G	4: 74,295,906 (GRCm39)	T882A	probably damaging	Het
Kif1a	G	T	1: 92,967,496 (GRCm39)	F1138L	probably damaging	Het
Klhl20	A	T	1: 160,934,307 (GRCm39)	S237R	probably benign	Het
Lamc1	A	T	1: 153,123,014 (GRCm39)	N725K	probably damaging	Het
Lmtk3	A	G	7: 45,444,890 (GRCm39)	D1191G	unknown	Het
Ltbp1	C	A	17: 75,670,358 (GRCm39)	N1466K	possibly damaging	Het
Ly75	T	C	2: 60,195,432 (GRCm39)	E242G	probably damaging	Het
Lyrm1	T	C	7: 119,515,449 (GRCm39)	V113A	probably benign	Het
Mfsd13a	G	T	19: 46,360,446 (GRCm39)	A333S	probably benign	Het
Mllt10	T	C	2: 18,167,214 (GRCm39)	S380P	possibly damaging	Het
Mrc2	A	G	11: 105,238,829 (GRCm39)	K1295E	possibly damaging	Het
Muc5ac	A	T	7: 141,363,528 (GRCm39)	I2280F	unknown	Het
Neurod2	A	C	11: 98,218,023 (GRCm39)	F380L	probably damaging	Het
Ntrk3	G	A	7: 78,005,954 (GRCm39)	A469V	probably damaging	Het
Nup205	T	C	6: 35,175,888 (GRCm39)	F584L	probably damaging	Het
Oas1d	A	T	5: 121,057,210 (GRCm39)	Y272F	probably damaging	Het
Olfm3	T	C	3: 114,874,794 (GRCm39)	V30A	probably benign	Het
Or4c110	T	A	2: 88,831,973 (GRCm39)	I220F	probably damaging	Het
Or5b117	A	G	19: 13,431,563 (GRCm39)	I106T	probably benign	Het
Or8k22	A	G	2: 86,163,064 (GRCm39)	V212A	probably benign	Het
Pcdhga12	A	G	18: 37,901,427 (GRCm39)	Y753C	probably damaging	Het
Phox2b	A	G	5: 67,253,514 (GRCm39)	V294A	unknown	Het
Prdm2	A	T	4: 142,859,812 (GRCm39)	C1159*	probably null	Het
Ptpn12	G	T	5: 21,207,631 (GRCm39)	S275*	probably null	Het
Rigi	T	C	4: 40,209,894 (GRCm39)	M725V	probably damaging	Het
Rnf223	A	T	4: 156,216,776 (GRCm39)	E50D	probably damaging	Het
Rrp12	A	T	19: 41,879,548 (GRCm39)	Y169N	probably benign	Het
Sgip1	T	C	4: 102,757,736 (GRCm39)		probably null	Het
Shank2	T	C	7: 143,964,798 (GRCm39)	I802T	probably damaging	Het
Skint2	A	T	4: 112,481,329 (GRCm39)	N64I	probably damaging	Het
Tmem106c	G	C	15: 97,865,985 (GRCm39)	G192R	probably damaging	Het
Tmem72	T	C	6: 116,673,800 (GRCm39)	H106R	probably damaging	Het
Upf2	G	C	2: 6,030,926 (GRCm39)	V789L	unknown	Het
Vash1	A	G	12: 86,726,758 (GRCm39)		probably benign	Het
Vmn1r201	T	A	13: 22,658,875 (GRCm39)	Y30N	probably benign	Het
Xpr1	A	G	1: 155,166,035 (GRCm39)	F571L	possibly damaging	Het
Yif1a	T	C	19: 5,139,815 (GRCm39)	S87P	probably damaging	Het
Zer1	T	C	2: 29,997,520 (GRCm39)	Y462C	probably damaging	Het
Zfp597	G	A	16: 3,684,375 (GRCm39)	P127L	possibly damaging	Het
Zxdc	T	C	6: 90,375,749 (GRCm39)	S742P	probably benign	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
R7394:Smpd3	UTSW	8	106,991,642 (GRCm39)	missense	probably damaging	0.99
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
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'- TAGCTCCAAAGAGAAGTGCTC -3'
(R):5'- GCACAGAACTTTAGCTTGTTTCCC -3'

Sequencing Primer
(F):5'- CTCTGTGAAGGGGAGTGCC -3'
(R):5'- AGAACTTTAGCTTGTTTCCCTTCTG -3'

Posted On

2020-09-15