Mutagenetix > Incidental Mutation

Incidental Mutation 'R7974:Smpd3'

650780

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

046017-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.922) question?

Stock #

R7974 (G1)

Quality Score

225.009

Status

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: 99.9%
10x: 99.7%
20x: 99.0%

Validation Efficiency

100% (64/64)

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
Ablim1	C	T	19: 57,033,405 (GRCm39)		probably null	Het
Adamts19	A	T	18: 59,144,094 (GRCm39)	Q892L	possibly damaging	Het
Adamts9	A	G	6: 92,886,668 (GRCm39)		probably null	Het
Aftph	T	C	11: 20,648,233 (GRCm39)	*686W	probably null	Het
AI661453	T	C	17: 47,777,006 (GRCm39)	L244P	unknown	Het
Ankar	C	A	1: 72,738,138 (GRCm39)	E15*	probably null	Het
Ankrd39	A	G	1: 36,585,999 (GRCm39)		probably benign	Het
Arsi	A	G	18: 61,045,478 (GRCm39)	D56G	probably damaging	Het
Blmh	T	C	11: 76,856,729 (GRCm39)	I245T	possibly damaging	Het
Ccr6	T	C	17: 8,475,056 (GRCm39)	F87S	probably damaging	Het
Cdc42ep2	T	C	19: 5,968,523 (GRCm39)	K61E	probably damaging	Het
Celsr1	C	T	15: 85,915,231 (GRCm39)	G914D	probably damaging	Het
Cep126	T	A	9: 8,120,764 (GRCm39)	K86N	probably benign	Het
Cfap70	A	T	14: 20,470,818 (GRCm39)	F532I	probably damaging	Het
Cpsf3	T	A	12: 21,358,006 (GRCm39)	L506Q	probably damaging	Het
Dct	A	C	14: 118,277,067 (GRCm39)	I273S	probably damaging	Het
Dsel	T	C	1: 111,788,229 (GRCm39)	I769V	probably benign	Het
Dus2	G	A	8: 106,762,652 (GRCm39)	E138K	probably benign	Het
Emsy	A	G	7: 98,279,425 (GRCm39)	S305P	possibly damaging	Het
Erp27	A	T	6: 136,885,063 (GRCm39)	V245D	probably damaging	Het
Fez1	C	A	9: 36,755,244 (GRCm39)	T81K	probably damaging	Het
Gli3	A	C	13: 15,900,841 (GRCm39)	Q1409H	probably benign	Het
Hdac9	T	C	12: 34,353,219 (GRCm39)	S664G	possibly damaging	Het
Hibadh	A	G	6: 52,534,880 (GRCm39)	S167P	probably benign	Het
Hsdl1	A	G	8: 120,293,072 (GRCm39)	V121A	probably benign	Het
Ift70a1	T	C	2: 75,810,688 (GRCm39)	H465R	probably damaging	Het
Ighv1-18	A	C	12: 114,646,669 (GRCm39)	I6S	possibly damaging	Het
Iqcm	T	A	8: 76,281,520 (GRCm39)	M1K	probably null	Het
Itch	T	C	2: 155,034,079 (GRCm39)	F417S	probably damaging	Het
Itpr1	C	T	6: 108,500,366 (GRCm39)	T2653I	possibly damaging	Het
Kank1	T	G	19: 25,401,584 (GRCm39)	Y1064D	probably damaging	Het
Kmt2c	T	C	5: 25,505,561 (GRCm39)	Q3249R	probably damaging	Het
Lefty1	T	C	1: 180,765,385 (GRCm39)	C318R	probably damaging	Het
Lmbr1l	C	T	15: 98,809,500 (GRCm39)	V147I	probably benign	Het
Meig1	C	A	2: 3,412,911 (GRCm39)	E37*	probably null	Het
Mpp3	A	G	11: 101,899,180 (GRCm39)		probably null	Het
Muc17	T	C	5: 137,175,664 (GRCm39)	N2S		Het
Mup7	T	C	4: 60,067,518 (GRCm39)	E199G	possibly damaging	Het
Nol4	G	C	18: 22,852,082 (GRCm39)	Y275*	probably null	Het
Nrxn1	G	A	17: 91,008,207 (GRCm39)	P429S	probably damaging	Het
Or14j8	T	C	17: 38,263,672 (GRCm39)	Y81C	probably damaging	Het
Pfkl	A	T	10: 77,829,996 (GRCm39)	F367L	probably damaging	Het
Pik3cg	T	C	12: 32,254,031 (GRCm39)	E652G	probably benign	Het
Prkag3	A	G	1: 74,783,980 (GRCm39)	I301T	probably benign	Het
Rcn1	G	A	2: 105,224,055 (GRCm39)	P163L	probably benign	Het
Slc1a7	G	A	4: 107,869,473 (GRCm39)	V513M	probably benign	Het
Slc37a2	A	T	9: 37,150,421 (GRCm39)		probably null	Het
Slc9b1	C	T	3: 135,099,791 (GRCm39)	T437I	possibly damaging	Het
Smap1	T	G	1: 23,888,522 (GRCm39)	T248P	probably benign	Het
Spata20	T	C	11: 94,374,966 (GRCm39)	N212S	possibly damaging	Het
Sphkap	A	C	1: 83,256,683 (GRCm39)	C355W	probably damaging	Het
Spopfm2	T	C	3: 94,082,848 (GRCm39)	K321R	probably benign	Het
Spsb1	T	A	4: 149,991,566 (GRCm39)	M1L	probably damaging	Het
Srebf2	C	T	15: 82,062,966 (GRCm39)	R468C	probably damaging	Het
Stxbp5	A	C	10: 9,646,439 (GRCm39)		probably null	Het
Taar5	G	C	10: 23,847,120 (GRCm39)	D173H	possibly damaging	Het
Tfrc	A	G	16: 32,440,101 (GRCm39)	D438G	probably null	Het
Tinag	A	T	9: 76,907,131 (GRCm39)	I368K	probably benign	Het
Tm9sf1	A	G	14: 55,873,906 (GRCm39)	W531R	probably damaging	Het
Tnc	G	T	4: 63,918,961 (GRCm39)	P1154Q	possibly damaging	Het
Toporsl	A	G	4: 52,611,645 (GRCm39)	R513G	probably damaging	Het
Vat1	A	G	11: 101,356,956 (GRCm39)	S2P	probably benign	Het
Vmn2r107	C	G	17: 20,577,270 (GRCm39)	P423A	probably benign	Het
Vmn2r2	T	A	3: 64,024,808 (GRCm39)	E591V	probably damaging	Het
Vmn2r62	T	A	7: 42,437,281 (GRCm39)	Y401F	probably damaging	Het
Vmn2r62	G	A	7: 42,414,031 (GRCm39)	T804I	probably damaging	Het
Vmn2r89	A	T	14: 51,693,459 (GRCm39)	I270F	probably damaging	Het
Zfp418	T	C	7: 7,185,167 (GRCm39)	F377L	possibly damaging	Het
Zkscan5	T	C	5: 145,144,502 (GRCm39)	S182P	unknown	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
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'- AGCTCCAAAGAGAAGTGCTC -3'
(R):5'- GCACAGAACTTTAGCTTGTTTCC -3'

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

Posted On

2020-09-15