Mutagenetix > Incidental Mutation

Incidental Mutation 'R6891:Smpd3'

537219

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

044985-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.904) question?

Stock #

R6891 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

106979180-107064597 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 106991300 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Tyrosine to Histidine at position 418 (Y418H)

Ref Sequence

ENSEMBL: ENSMUSP00000148282 (fasta)

Gene Model

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

AlphaFold

Q9JJY3

Predicted Effect

probably damaging
Transcript: ENSMUST00000067512
AA Change: Y418H

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000069255
Gene: ENSMUSG00000031906
AA Change: Y418H

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: Y418H

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.4%
20x: 98.0%

Validation Efficiency

97% (72/74)

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: 72 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Actl11	C	T	9: 107,806,346 (GRCm39)	A223V	probably benign	Het
Agbl5	G	T	5: 31,052,522 (GRCm39)	R61L	probably damaging	Het
Agmat	A	T	4: 141,483,192 (GRCm39)	T209S	probably benign	Het
Ankrd34a	G	A	3: 96,505,335 (GRCm39)	V180I	probably benign	Het
Anks1	C	T	17: 28,276,398 (GRCm39)	T1047M	probably damaging	Het
Arhgap21	T	A	2: 20,855,142 (GRCm39)	I1407F	probably damaging	Het
Armc1	C	A	3: 19,189,205 (GRCm39)	C183F	probably damaging	Het
Atg13	A	G	2: 91,516,136 (GRCm39)	M196T	probably benign	Het
AU040320	G	T	4: 126,740,231 (GRCm39)	S864I	possibly damaging	Het
Btn2a2	T	C	13: 23,667,014 (GRCm39)	D197G	probably benign	Het
Carmil1	A	G	13: 24,325,706 (GRCm39)	I208T	probably benign	Het
Cbs	T	A	17: 31,841,431 (GRCm39)	R263S	probably damaging	Het
Ccdc7a	C	A	8: 129,753,119 (GRCm39)	R204L	probably damaging	Het
Cdhr1	A	T	14: 36,819,334 (GRCm39)		probably null	Het
Cers4	G	A	8: 4,573,731 (GRCm39)	R378Q	probably damaging	Het
Chst1	T	G	2: 92,444,088 (GRCm39)	L187V	probably benign	Het
Clec4e	A	T	6: 123,260,565 (GRCm39)	N164K	probably damaging	Het
Cln3	T	A	7: 126,181,975 (GRCm39)	D29V	possibly damaging	Het
Crybg2	A	G	4: 133,809,148 (GRCm39)	S187G	probably benign	Het
Ddx1	A	T	12: 13,286,096 (GRCm39)	N285K	probably benign	Het
Dmxl2	A	G	9: 54,387,664 (GRCm39)	I58T	probably damaging	Het
Dock4	A	G	12: 40,829,135 (GRCm39)	Y1007C	probably damaging	Het
Eral1	C	T	11: 77,966,559 (GRCm39)	V234I	possibly damaging	Het
Fads2b	C	A	2: 85,319,149 (GRCm39)	M384I	possibly damaging	Het
Fads2b	T	G	2: 85,319,157 (GRCm39)	T382P	probably damaging	Het
Fam161b	A	G	12: 84,401,554 (GRCm39)	F400S	probably damaging	Het
Fmnl3	T	C	15: 99,223,754 (GRCm39)	D314G	probably damaging	Het
Foxred2	A	T	15: 77,839,909 (GRCm39)	L127Q	probably damaging	Het
Gjd2	G	A	2: 113,843,575 (GRCm39)	A14V	possibly damaging	Het
Gon4l	A	G	3: 88,766,173 (GRCm39)		probably null	Het
Gpr151	T	A	18: 42,711,985 (GRCm39)	D231V	probably benign	Het
Gzf1	A	T	2: 148,526,689 (GRCm39)	K387*	probably null	Het
Hfm1	T	A	5: 107,065,240 (GRCm39)	K146N	possibly damaging	Het
Hgf	G	A	5: 16,809,920 (GRCm39)		probably null	Het
Isoc2b	A	G	7: 4,854,487 (GRCm39)	S15P	probably damaging	Het
Itga5	A	G	15: 103,265,970 (GRCm39)	S126P	probably damaging	Het
Kat6b	A	G	14: 21,719,104 (GRCm39)	D1152G	probably benign	Het
Kcna4	C	T	2: 107,126,652 (GRCm39)	S462F	probably damaging	Het
Kif24	A	T	4: 41,394,168 (GRCm39)	C902S	probably benign	Het
Lama2	A	T	10: 27,204,068 (GRCm39)	C523*	probably null	Het
Lama2	G	C	10: 27,204,078 (GRCm39)	S520*	probably null	Het
Ltf	T	C	9: 110,854,181 (GRCm39)	V332A	probably benign	Het
Mapkap1	T	C	2: 34,453,153 (GRCm39)	F349L	probably damaging	Het
Mdm1	A	G	10: 117,983,937 (GRCm39)	N188D	probably benign	Het
Mfn1	T	C	3: 32,631,252 (GRCm39)	S730P	possibly damaging	Het
Mrgprd	T	A	7: 144,876,087 (GRCm39)	D319E	probably benign	Het
Mrps9	C	A	1: 42,944,573 (GRCm39)	L364I	probably damaging	Het
Myo1h	C	T	5: 114,487,673 (GRCm39)	R626C	probably damaging	Het
Nme3	T	C	17: 25,115,829 (GRCm39)	S61P	probably benign	Het
Or2g1	A	G	17: 38,106,395 (GRCm39)	Q20R	probably benign	Het
Or52e18	A	G	7: 104,609,192 (GRCm39)	I249T	probably damaging	Het
Pald1	A	G	10: 61,184,311 (GRCm39)		probably null	Het
Papola	A	T	12: 105,775,950 (GRCm39)		probably benign	Het
Peg10	GAT	GATCAT	6: 4,756,449 (GRCm39)		probably benign	Het
Plch1	T	C	3: 63,605,504 (GRCm39)	T1458A	probably benign	Het
Polr3e	A	G	7: 120,543,873 (GRCm39)	Q659R	probably damaging	Het
Pramel38	C	A	5: 94,365,978 (GRCm39)	P32Q	probably damaging	Het
Shoc2	T	C	19: 53,976,548 (GRCm39)	V146A	probably benign	Het
Slc15a1	T	C	14: 121,713,442 (GRCm39)	T362A	probably benign	Het
Sorcs1	A	T	19: 50,213,557 (GRCm39)	C723*	probably null	Het
Supt7l	T	A	5: 31,680,365 (GRCm39)	N16Y	probably damaging	Het
Syngr2	T	C	11: 117,703,499 (GRCm39)	V105A	probably damaging	Het
Thrb	T	A	14: 17,981,899 (GRCm38)	V8E	probably benign	Het
Tlx1	A	T	19: 45,139,757 (GRCm39)	I135F	probably damaging	Het
Tnfaip3	A	G	10: 18,887,417 (GRCm39)	I36T	probably damaging	Het
Troap	A	G	15: 98,980,569 (GRCm39)	Y583C	possibly damaging	Het
Usp17lb	T	C	7: 104,490,307 (GRCm39)	K207E	probably benign	Het
Vmn2r10	C	T	5: 109,149,845 (GRCm39)	V400M	probably damaging	Het
Wdr49	A	T	3: 75,240,590 (GRCm39)		probably null	Het
Wdr64	G	T	1: 175,533,634 (GRCm39)	W90L	probably damaging	Het
Yme1l1	A	G	2: 23,085,401 (GRCm39)	E662G	probably damaging	Het
Zfp334	C	T	2: 165,224,644 (GRCm39)	V68I	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
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
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'- CCTGAGTTCAGTTCCATGAAAGG -3'
(R):5'- GCAGGAGGTGTTTGACAAGC -3'

Sequencing Primer
(F):5'- TCCCATCAAGCGAGTGAGGATTC -3'
(R):5'- TTTGACAAGCGTGCGGC -3'

Posted On

2018-10-18