Mutagenetix > Incidental Mutation

Incidental Mutation 'R8264:Smpd3'

639731

Institutional Source

Beutler Lab

Gene Symbol

Smpd3

Ensembl Gene

ENSMUSG00000031906

Gene Name

sphingomyelin phosphodiesterase 3, neutral

Synonyms

neutral sphingomyelinase II, nSMase2, fro, 4631433G07Rik

MMRRC Submission

Accession Numbers

Essential gene?

Probably essential (E-score: 0.893) question?

Stock #

R8264 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

106252548-106337988 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 106264658 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Tyrosine to Cysteine at position 421 (Y421C)

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: Y421C

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

SMART Domains

Protein: ENSMUSP00000069255
Gene: ENSMUSG00000031906
AA Change: Y421C

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: Y421C

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

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.6%
20x: 98.8%

Validation Efficiency

98% (51/52)

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: 50 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1110002E22Rik	T	A	3: 138,067,782	C911S	probably damaging	Het
Abcc4	T	A	14: 118,594,842	N792I	possibly damaging	Het
Acacb	A	T	5: 114,207,366	H960L	probably benign	Het
Aox1	A	G	1: 58,053,714	T162A	possibly damaging	Het
Cacna1g	T	C	11: 94,473,566	S18G	probably benign	Het
Chfr	T	A	5: 110,152,434	I348N	possibly damaging	Het
Cntln	G	A	4: 85,098,411	R12Q	probably damaging	Het
Cyp2c40	A	G	19: 39,807,527	S136P	possibly damaging	Het
Dnah14	T	A	1: 181,744,792	M2896K	probably damaging	Het
Elp6	A	G	9: 110,319,687	T215A	probably damaging	Het
Esyt2	A	C	12: 116,365,920	Q699H	probably benign	Het
Fbxo25	A	G	8: 13,929,393	T204A	possibly damaging	Het
Fhdc1	A	G	3: 84,455,032	S294P	probably damaging	Het
G530012D18Rik	C	G	1: 85,577,214	D113E	unknown	Het
Galnt10	A	G	11: 57,782,206	I463V	probably benign	Het
Glce	A	G	9: 62,060,430	F480L	probably benign	Het
H2-Aa	A	G	17: 34,287,735	V11A	probably benign	Het
Hsd17b4	A	G	18: 50,146,526	T191A	possibly damaging	Het
Itpr3	G	T	17: 27,104,112		silent	Het
Izumo4	G	T	10: 80,702,738	G8V		Het
Klk1b5	T	A	7: 44,220,030	L178H	probably damaging	Het
Lama2	T	C	10: 27,467,222	N85D	probably benign	Het
Liph	A	C	16: 21,983,971	I116R	possibly damaging	Het
Lpar5	T	A	6: 125,081,502	V62D	probably damaging	Het
Map3k19	T	A	1: 127,823,791	I303F		Het
Mymk	A	G	2: 27,067,856		probably benign	Het
Myo10	G	A	15: 25,800,109	V1424M	probably damaging	Het
Myof	T	G	19: 37,921,433	Q1528P	probably damaging	Het
Ncapd3	T	C	9: 27,094,742		probably benign	Het
Nup214	T	A	2: 31,994,726	Y500N	possibly damaging	Het
Olfr1040	T	C	2: 86,146,194	D180G	probably damaging	Het
Papd4	C	T	13: 93,175,569	G208S	probably damaging	Het
Pappa2	T	C	1: 158,854,973	Y835C	probably damaging	Het
Pcdh18	T	C	3: 49,756,581	E95G	probably damaging	Het
Phf3	A	T	1: 30,831,057	N303K	possibly damaging	Het
Pnn	C	T	12: 59,072,577	H649Y	unknown	Het
Rab11fip1	G	A	8: 27,152,480	Q764*	probably null	Het
Ralgapa2	A	T	2: 146,333,450	M1762K	possibly damaging	Het
Rif1	G	A	2: 52,090,278	A496T	noncoding transcript	Het
Rnase13	A	T	14: 51,922,457	V75D	probably damaging	Het
Sema3c	G	A	5: 17,676,539		probably benign	Het
Sema4c	C	G	1: 36,552,885	G266R	probably damaging	Het
Slfn5	A	T	11: 82,956,550	D87V	probably damaging	Het
Snrnp40	T	C	4: 130,378,074	V188A	probably benign	Het
Srms	A	G	2: 181,212,550	Y75H	probably benign	Het
Tex15	T	C	8: 33,582,362	S2646P	probably benign	Het
Togaram1	A	G	12: 64,995,556	I1130V	probably benign	Het
Ttf1	A	G	2: 29,064,677	K18E	possibly damaging	Het
Unc5b	G	T	10: 60,768,334	T827K	probably benign	Het
Zfhx2	T	A	14: 55,065,512	T1672S	possibly damaging	Het

Other mutations in Smpd3

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL03380:Smpd3	APN	8	106259659	missense	probably benign	0.01
BB010:Smpd3	UTSW	8	106255622	missense	probably benign
BB020:Smpd3	UTSW	8	106255622	missense	probably benign
G1citation:Smpd3	UTSW	8	106265964	start gained	probably benign
R0240:Smpd3	UTSW	8	106265156	missense	probably damaging	0.96
R0240:Smpd3	UTSW	8	106265156	missense	probably damaging	0.96
R0456:Smpd3	UTSW	8	106259656	missense	probably benign
R0759:Smpd3	UTSW	8	106265228	missense	probably benign	0.34
R0799:Smpd3	UTSW	8	106264789	missense	possibly damaging	0.92
R1544:Smpd3	UTSW	8	106265567	missense	possibly damaging	0.70
R1756:Smpd3	UTSW	8	106264971	missense	probably benign
R2937:Smpd3	UTSW	8	106264820	missense	probably damaging	1.00
R2939:Smpd3	UTSW	8	106257407	missense	probably benign	0.00
R4614:Smpd3	UTSW	8	106259739	missense	probably damaging	1.00
R5829:Smpd3	UTSW	8	106264880	missense	probably benign	0.15
R6822:Smpd3	UTSW	8	106265964	start gained	probably benign
R6891:Smpd3	UTSW	8	106264668	missense	probably damaging	1.00
R6962:Smpd3	UTSW	8	106265219	missense	probably benign	0.34
R6965:Smpd3	UTSW	8	106259881	missense	probably damaging	1.00
R7344:Smpd3	UTSW	8	106265193	missense	probably damaging	1.00
R7394:Smpd3	UTSW	8	106265010	missense	probably damaging	0.99
R7823:Smpd3	UTSW	8	106255622	missense	probably benign
R7825:Smpd3	UTSW	8	106255622	missense	probably benign
R7933:Smpd3	UTSW	8	106255622	missense	probably benign
R7974:Smpd3	UTSW	8	106255622	missense	probably benign
R7975:Smpd3	UTSW	8	106255622	missense	probably benign
R7976:Smpd3	UTSW	8	106255622	missense	probably benign
R7977:Smpd3	UTSW	8	106259894	missense	probably benign	0.11
R7987:Smpd3	UTSW	8	106259894	missense	probably benign	0.11
R8260:Smpd3	UTSW	8	106257415	missense	probably benign	0.13
R8292:Smpd3	UTSW	8	106264790	missense	probably benign	0.08
R8432:Smpd3	UTSW	8	106257677	critical splice acceptor site	probably null
R8494:Smpd3	UTSW	8	106255350	missense	probably damaging	0.99
R8779:Smpd3	UTSW	8	106265489	missense	probably benign	0.37
R8787:Smpd3	UTSW	8	106255745	missense	probably damaging	1.00
R9005:Smpd3	UTSW	8	106257426	missense	probably benign	0.02
R9008:Smpd3	UTSW	8	106257426	missense	probably benign	0.02
R9355:Smpd3	UTSW	8	106265193	missense	probably damaging	1.00
R9516:Smpd3	UTSW	8	106265487	missense	probably benign	0.03
R9698:Smpd3	UTSW	8	106265664	missense	possibly damaging	0.54
R9703:Smpd3	UTSW	8	106265081	missense	probably damaging	0.99
Z1177:Smpd3	UTSW	8	106264842	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- CTGAGTTCAGTTCCATGAAAGGC -3'
(R):5'- TGCAGGAGGTGTTTGACAAGC -3'

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

Posted On

2020-07-28