Mutagenetix > Incidental Mutation

Incidental Mutation 'R6962:Smpd3'

541827

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

045072-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.922) question?

Stock #

R6962 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

106979180-107064597 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 106991851 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Aspartic acid to Glycine at position 234 (D234G)

Ref Sequence

ENSEMBL: ENSMUSP00000148282 (fasta)

Gene Model

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

AlphaFold

Q9JJY3

Predicted Effect

probably benign
Transcript: ENSMUST00000067512
AA Change: D234G

PolyPhen 2 Score 0.336 (Sensitivity: 0.90; Specificity: 0.89)

SMART Domains

Protein: ENSMUSP00000069255
Gene: ENSMUSG00000031906
AA Change: D234G

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: ENSMUST00000212896
AA Change: D234G

PolyPhen 2 Score 0.336 (Sensitivity: 0.90; Specificity: 0.89)

Meta Mutation Damage Score

0.0600

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.2%
20x: 97.2%

Validation Efficiency

96% (74/77)

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: 76 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4930407I10Rik	A	G	15: 81,949,150 (GRCm39)	K1016E	probably benign	Het
Abca3	T	C	17: 24,583,700 (GRCm39)	F30L	probably benign	Het
Arhgap17	C	T	7: 122,895,655 (GRCm39)	G490R	probably damaging	Het
Arsg	T	A	11: 109,412,495 (GRCm39)	L140H	probably damaging	Het
Bmp2k	T	A	5: 97,179,097 (GRCm39)	C130*	probably null	Het
C4b	T	C	17: 34,951,140 (GRCm39)		probably null	Het
Cdk5r2	A	G	1: 74,894,975 (GRCm39)	Y240C	probably damaging	Het
Cntnap5b	A	G	1: 100,202,197 (GRCm39)	E348G	probably benign	Het
Col27a1	A	G	4: 63,237,738 (GRCm39)		probably benign	Het
Cubn	G	A	2: 13,352,840 (GRCm39)	S1966F	probably benign	Het
Dnajc13	T	C	9: 104,058,208 (GRCm39)	Y1509C	probably benign	Het
Dpp4	A	G	2: 62,203,174 (GRCm39)	V265A	probably benign	Het
Dync2i1	A	T	12: 116,175,398 (GRCm39)	D926E	probably damaging	Het
Fbxl8	C	A	8: 105,995,338 (GRCm39)	N283K	possibly damaging	Het
Fev	T	A	1: 74,921,299 (GRCm39)	Q122L	probably benign	Het
Fgd4	T	A	16: 16,301,951 (GRCm39)		probably null	Het
Fnip2	A	C	3: 79,396,610 (GRCm39)	L439R	probably damaging	Het
Git1	C	A	11: 77,395,469 (GRCm39)	Q389K	probably benign	Het
Gm10509	C	G	17: 21,909,833 (GRCm39)	I53M	possibly damaging	Het
Gm5773	A	T	3: 93,681,234 (GRCm39)	H302L	possibly damaging	Het
Greb1l	G	T	18: 10,547,327 (GRCm39)	R1515L	probably damaging	Het
Gsc2	T	C	16: 17,732,902 (GRCm39)	Y2C	possibly damaging	Het
H60b	A	G	10: 22,162,053 (GRCm39)	N93D	probably benign	Het
Hgf	G	A	5: 16,820,752 (GRCm39)	R633Q	probably benign	Het
Hmgb1	C	T	5: 148,985,633 (GRCm39)		probably benign	Het
Hmmr	T	C	11: 40,598,242 (GRCm39)	T657A	probably damaging	Het
Htt	G	T	5: 35,057,115 (GRCm39)		probably null	Het
Ift80	G	A	3: 68,901,878 (GRCm39)		probably benign	Het
Kcnq5	G	T	1: 21,576,017 (GRCm39)	T229K	probably damaging	Het
Kcp	C	T	6: 29,482,839 (GRCm39)	R1410Q	probably benign	Het
Klhl30	T	G	1: 91,285,137 (GRCm39)	V331G	probably damaging	Het
Lrit1	G	C	14: 36,782,052 (GRCm39)	V242L	probably damaging	Het
Lrrc37	G	A	11: 103,505,126 (GRCm39)	P105S	possibly damaging	Het
Macf1	C	T	4: 123,334,515 (GRCm39)	R2849Q	probably benign	Het
Mex3b	T	G	7: 82,518,473 (GRCm39)	S263A	probably benign	Het
Mrgpre	A	G	7: 143,334,799 (GRCm39)	S235P	probably damaging	Het
Myh14	A	T	7: 44,307,363 (GRCm39)	V226D	probably benign	Het
Myom2	G	A	8: 15,167,741 (GRCm39)	A1109T	probably null	Het
Nudt8	G	T	19: 4,051,831 (GRCm39)	L147F	probably damaging	Het
Or2aj5	T	A	16: 19,424,672 (GRCm39)	I249L	probably benign	Het
Or52e8	T	A	7: 104,624,580 (GRCm39)	N208I	probably benign	Het
Or5w17	A	G	2: 87,584,071 (GRCm39)	Y89H	probably benign	Het
Or6z7	A	T	7: 6,484,008 (GRCm39)	I49N	probably benign	Het
P4htm	C	A	9: 108,456,394 (GRCm39)	A469S	possibly damaging	Het
Pld4	A	T	12: 112,733,288 (GRCm39)	H288L	probably benign	Het
Pnpla1	T	A	17: 29,097,455 (GRCm39)	I207N	probably damaging	Het
Ppcs	T	G	4: 119,279,375 (GRCm39)	N59T	probably damaging	Het
Ppm1k	A	T	6: 57,492,645 (GRCm39)	C214S	probably damaging	Het
Psg25	C	T	7: 18,263,679 (GRCm39)	G48E	probably damaging	Het
Rassf7	A	G	7: 140,797,503 (GRCm39)	T239A	possibly damaging	Het
Rgs3	G	T	4: 62,618,952 (GRCm39)		probably benign	Het
Scaper	T	C	9: 55,767,055 (GRCm39)	T465A	probably benign	Het
Slc4a7	G	T	14: 14,746,021 (GRCm38)	G405C	probably damaging	Het
Spata31f1e	T	C	4: 42,793,323 (GRCm39)	T270A	probably damaging	Het
Ssc4d	A	G	5: 135,991,775 (GRCm39)		probably null	Het
Sugct	G	T	13: 17,032,606 (GRCm39)		probably null	Het
Taok2	C	A	7: 126,466,088 (GRCm39)		probably null	Het
Tbx20	A	G	9: 24,681,036 (GRCm39)	V152A	probably damaging	Het
Tbx4	A	G	11: 85,781,085 (GRCm39)	E66G	probably benign	Het
Thbs2	T	C	17: 14,902,082 (GRCm39)	E382G	probably benign	Het
Ticrr	T	G	7: 79,315,645 (GRCm39)	S300A	possibly damaging	Het
Trim46	A	G	3: 89,146,303 (GRCm39)	L396P	probably damaging	Het
Trim56	A	G	5: 137,141,501 (GRCm39)	F672L	probably damaging	Het
Ttf2	A	G	3: 100,858,453 (GRCm39)	L712S	probably damaging	Het
Unc93b1	T	G	19: 3,986,303 (GRCm39)	D112E	possibly damaging	Het
Usp17lc	T	C	7: 103,068,118 (GRCm39)	L471P	probably benign	Het
Vmn2r85	A	G	10: 130,261,452 (GRCm39)	I295T	probably damaging	Het
Vmn2r96	T	G	17: 18,818,283 (GRCm39)	I812S	probably damaging	Het
Wdr7	G	A	18: 63,998,359 (GRCm39)	C1102Y	possibly damaging	Het
Wnt9b	G	T	11: 103,624,515 (GRCm39)	Q92K	probably null	Het
Zbtb26	A	T	2: 37,326,106 (GRCm39)	M310K	possibly damaging	Het
Zdhhc1	T	C	8: 106,210,279 (GRCm39)	H46R	probably damaging	Het
Zfp628	G	T	7: 4,922,549 (GRCm39)	R257L	probably benign	Het
Zfp747l1	A	T	7: 126,983,487 (GRCm39)	D538E	possibly damaging	Het
Zmat4	A	G	8: 24,392,181 (GRCm39)	T46A	probably benign	Het
Zmiz2	T	A	11: 6,352,455 (GRCm39)	W637R	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
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
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'- AGAGGTCTTATACAGCAGCTTGC -3'
(R):5'- ATCAGTGCAGCCAGCTTCAG -3'

Sequencing Primer
(F):5'- TTCACCAAGGACTCCCTGGAG -3'
(R):5'- TTCAGCAGCCTGGTGTCG -3'

Posted On

2018-11-28