Mutagenetix > Incidental Mutation

Incidental Mutation 'R7733:Sptlc3'

595963

Institutional Source

Beutler Lab

Gene Symbol

Sptlc3

Ensembl Gene

ENSMUSG00000039092

Gene Name

serine palmitoyltransferase, long chain base subunit 3

Synonyms

MMRRC Submission

045789-MU

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.101) question?

Stock #

R7733 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

139493913-139637674 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

G to T at 139631368 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Methionine to Isoleucine at position 512 (M512I)

Ref Sequence

ENSEMBL: ENSMUSP00000048313 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000047370] [ENSMUST00000110083]

AlphaFold

Q8BG54

Predicted Effect

possibly damaging
Transcript: ENSMUST00000047370
AA Change: M512I

PolyPhen 2 Score 0.773 (Sensitivity: 0.85; Specificity: 0.92)

SMART Domains

Protein: ENSMUSP00000048313
Gene: ENSMUSG00000039092
AA Change: M512I

Domain	Start	End	E-Value	Type
transmembrane domain	60	79	N/A	INTRINSIC
Pfam:Aminotran_1_2	160	520	4.8e-59	PFAM

Predicted Effect

possibly damaging
Transcript: ENSMUST00000110083
AA Change: M512I

PolyPhen 2 Score 0.773 (Sensitivity: 0.85; Specificity: 0.92)

SMART Domains

Protein: ENSMUSP00000105710
Gene: ENSMUSG00000039092
AA Change: M512I

Domain	Start	End	E-Value	Type
transmembrane domain	60	79	N/A	INTRINSIC
Pfam:Aminotran_1_2	160	520	4.8e-59	PFAM

Meta Mutation Damage Score

0.2622

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.7%
20x: 99.3%

Validation Efficiency

100% (83/83)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The SPTLC3 gene encodes an isoform of the third subunit of serine palmitoyltransferase (SPT; EC 2.3.1.50), which catalyzes the rate-limiting step of the de novo synthesis of sphingolipids (Hornemann et al., 2006 [PubMed 17023427]). SPT contains 2 main subunits: the common SPTLC1 subunit (MIM 605712) and either SPTLC2 (MIM 605713) or its isoform SPTLC2L (SPTLC3), depending on the tissue in which biosynthesis occurs (Hornemann et al., 2006 [PubMed 17023427]). There are also 2 highly related isoforms of a third subunit, SSSPTA (MIM 613540) and SSSPTB (MIM 610412), that confer acyl-CoA preference of the SPT enzyme and are essential for maximal enzyme activity (Han et al., 2009 [PubMed 19416851]).[supplied by OMIM, Nov 2010]

Allele List at MGI

Other mutations in this stock

Total: 82 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
5530400C23Rik	T	A	6: 133,294,277	S95T	probably benign	Het
9530053A07Rik	A	T	7: 28,139,965	D401V	probably damaging	Het
Abca8a	A	G	11: 110,054,587	F1070L	probably benign	Het
Acsl3	G	C	1: 78,688,236		probably null	Het
Adarb2	T	A	13: 8,752,608	S640T	possibly damaging	Het
Adgre5	T	C	8: 83,729,396	D257G	probably benign	Het
Adora2b	A	T	11: 62,265,339	I205F	possibly damaging	Het
Asb14	A	G	14: 26,912,352	M505V	probably benign	Het
Atrnl1	T	C	19: 57,701,988	V876A	probably benign	Het
AU040320	A	G	4: 126,835,529	N495D	possibly damaging	Het
BC005561	T	C	5: 104,519,960	F783L	possibly damaging	Het
Bcam	A	T	7: 19,760,388	V361E	probably benign	Het
Cbwd1	T	C	19: 24,940,794	D204G	probably damaging	Het
Ccdc7a	T	A	8: 128,993,052	E247V	probably damaging	Het
Cd84	T	A	1: 171,840,659	M1K	probably null	Het
Cfap43	C	T	19: 47,897,993	R61H	possibly damaging	Het
Clec4a1	A	G	6: 122,932,150	D159G	possibly damaging	Het
Ctcfl	C	T	2: 173,117,192	R247Q	probably benign	Het
Ctdnep1	G	A	11: 69,990,009	R236Q	probably damaging	Het
Cwf19l2	A	T	9: 3,450,066	H589L	probably benign	Het
Cyp2u1	G	T	3: 131,303,027	A34E	probably benign	Het
Cyp4x1	A	G	4: 115,120,194	S281P	possibly damaging	Het
Dag1	T	C	9: 108,208,848	T365A	probably benign	Het
Dhx57	A	T	17: 80,265,074		probably null	Het
Dnajb1	T	G	8: 83,608,377	S16A	probably benign	Het
Dsc2	A	T	18: 20,048,315	L145Q	probably benign	Het
Dsc2	G	C	18: 20,048,316	L145V	probably benign	Het
Eefsec	T	C	6: 88,376,220	T156A	possibly damaging	Het
Eif6	T	A	2: 155,823,232	D169V	probably benign	Het
Ell3	C	A	2: 121,442,520	G3V	possibly damaging	Het
Eprs	A	T	1: 185,397,161	H615L	probably benign	Het
Fbxw10	A	G	11: 62,873,397	Y630C	unknown	Het
G6pc2	C	T	2: 69,220,183	Q51*	probably null	Het
Glt8d1	C	T	14: 31,001,978		probably benign	Het
Gm16486	A	G	8: 70,717,451	T1397A	possibly damaging	Het
Gpr4	T	C	7: 19,222,710	Y186H	probably damaging	Het
Grhpr	T	C	4: 44,981,494		probably benign	Het
Gsdma3	A	G	11: 98,635,215	H264R	probably damaging	Het
Hcfc2	A	G	10: 82,739,179	Y224C	probably benign	Het
Helz2	A	G	2: 181,230,355	F2608S	possibly damaging	Het
Herc2	C	T	7: 56,188,664	T3313M	probably damaging	Het
Hmgcl	A	T	4: 135,960,083	H223L	probably benign	Het
Igf2r	A	G	17: 12,739,369	V139A	possibly damaging	Het
Kif5a	T	A	10: 127,236,740	T727S	probably benign	Het
Kifc1	G	A	17: 33,883,569	R357W	probably damaging	Het
Krt81	T	A	15: 101,463,514	S62C	probably damaging	Het
Lgi2	T	C	5: 52,538,531	N362S	probably benign	Het
Lig1	G	T	7: 13,296,231	R378L	possibly damaging	Het
Map3k13	C	T	16: 21,921,686	R588C	probably damaging	Het
Mov10l1	T	A	15: 89,024,801	F1008L	probably damaging	Het
Nr4a2	A	G	2: 57,112,321	V40A	probably benign	Het
Nrde2	A	T	12: 100,144,140	C206S	possibly damaging	Het
Olfr1316	C	T	2: 112,130,041	V257I	probably benign	Het
Parp1	T	C	1: 180,600,212		probably null	Het
Pcdhb12	A	G	18: 37,437,036	T412A	probably damaging	Het
Plekhh2	T	A	17: 84,583,524	Y839*	probably null	Het
Pnpla6	T	A	8: 3,522,660	F316I	probably benign	Het
Prcp	C	T	7: 92,901,298	T101M	probably damaging	Het
Prex2	G	T	1: 11,181,959	R1076L	probably benign	Het
Prpf40b	T	C	15: 99,308,343		probably null	Het
Psd3	T	G	8: 68,120,916	K204N	possibly damaging	Het
Ptpro	C	A	6: 137,414,286	C801*	probably null	Het
Ptprt	A	G	2: 161,575,787	V923A	probably damaging	Het
Ptprz1	T	A	6: 23,000,384	D824E	probably benign	Het
Rasgrf1	A	G	9: 89,981,727	D582G	probably benign	Het
Rfc2	T	C	5: 134,593,216	L183P	probably damaging	Het
Rnf114	T	C	2: 167,512,518	V173A	probably damaging	Het
Scn3a	T	A	2: 65,508,650	I562F	probably benign	Het
Setmar	T	C	6: 108,076,127	I194T	probably damaging	Het
Sptb	A	T	12: 76,597,921		probably null	Het
Sptbn2	C	G	19: 4,749,012	R2037G	probably benign	Het
Svep1	C	A	4: 58,049,239	A3423S	probably benign	Het
Sycp1	T	C	3: 102,895,962	T511A	probably benign	Het
Synm	T	A	7: 67,735,945		probably null	Het
Tada1	C	T	1: 166,389,942	P216L	probably damaging	Het
Tas2r117	T	A	6: 132,803,175	M92K	probably benign	Het
Thsd1	T	C	8: 22,258,721	L536P	probably damaging	Het
Timp2	T	G	11: 118,317,529		probably null	Het
Trak1	T	A	9: 121,367,225	V41D	possibly damaging	Het
Ubqln3	T	A	7: 104,141,076	L602F	probably damaging	Het
Vmn2r59	A	G	7: 42,012,019	F791L	probably benign	Het
Wbp4	A	G	14: 79,477,040		probably null	Het

Other mutations in Sptlc3

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01392:Sptlc3	APN	2	139546421	missense	possibly damaging	0.55
IGL01537:Sptlc3	APN	2	139589695	missense	possibly damaging	0.95
IGL01996:Sptlc3	APN	2	139581504	splice site	probably benign
IGL02512:Sptlc3	APN	2	139547203	missense	probably damaging	1.00
IGL03278:Sptlc3	APN	2	139589659	missense	probably damaging	1.00
IGL03286:Sptlc3	APN	2	139589659	missense	probably damaging	1.00
R0266:Sptlc3	UTSW	2	139596037	missense	possibly damaging	0.93
R0362:Sptlc3	UTSW	2	139546555	splice site	probably benign
R1464:Sptlc3	UTSW	2	139547234	missense	probably benign	0.00
R1464:Sptlc3	UTSW	2	139547234	missense	probably benign	0.00
R1494:Sptlc3	UTSW	2	139589560	missense	possibly damaging	0.58
R1847:Sptlc3	UTSW	2	139625923	missense	probably benign	0.08
R1919:Sptlc3	UTSW	2	139566675	missense	possibly damaging	0.66
R2093:Sptlc3	UTSW	2	139625874	missense	possibly damaging	0.89
R2396:Sptlc3	UTSW	2	139566586	missense	probably benign	0.44
R2972:Sptlc3	UTSW	2	139589661	missense	probably damaging	1.00
R2973:Sptlc3	UTSW	2	139589661	missense	probably damaging	1.00
R2974:Sptlc3	UTSW	2	139589661	missense	probably damaging	1.00
R4601:Sptlc3	UTSW	2	139636680	missense	probably benign	0.01
R4602:Sptlc3	UTSW	2	139636680	missense	probably benign	0.01
R4610:Sptlc3	UTSW	2	139636680	missense	probably benign	0.01
R4745:Sptlc3	UTSW	2	139547167	missense	probably damaging	1.00
R4779:Sptlc3	UTSW	2	139589589	missense	probably benign	0.04
R4992:Sptlc3	UTSW	2	139596003	missense	probably benign	0.04
R5162:Sptlc3	UTSW	2	139631343	missense	probably benign	0.11
R5401:Sptlc3	UTSW	2	139636723	missense	possibly damaging	0.75
R5406:Sptlc3	UTSW	2	139546478	missense	probably benign	0.26
R5642:Sptlc3	UTSW	2	139546408	missense	probably damaging	0.96
R5840:Sptlc3	UTSW	2	139547206	missense	probably damaging	1.00
R6057:Sptlc3	UTSW	2	139581613	missense	probably damaging	0.99
R6376:Sptlc3	UTSW	2	139636772	missense	probably benign	0.21
R6852:Sptlc3	UTSW	2	139566586	missense	probably benign	0.44
R7026:Sptlc3	UTSW	2	139537688	missense	probably benign
R7412:Sptlc3	UTSW	2	139589617	missense	possibly damaging	0.75
R7516:Sptlc3	UTSW	2	139589518	missense	probably benign	0.11
R7826:Sptlc3	UTSW	2	139547195	missense	probably benign	0.44
R7949:Sptlc3	UTSW	2	139625875	missense	possibly damaging	0.81
R9224:Sptlc3	UTSW	2	139494234	missense	probably benign	0.17
R9237:Sptlc3	UTSW	2	139566685	missense	probably benign	0.40
R9319:Sptlc3	UTSW	2	139636810	missense	possibly damaging	0.65
R9330:Sptlc3	UTSW	2	139546503	missense	probably benign

Predicted Primers

PCR Primer
(F):5'- CAGCAGGATAATTCTATCTTCCCTC -3'
(R):5'- GGATATTGCTGACATACCACAGTG -3'

Sequencing Primer
(F):5'- GATAATTCTATCTTCCCTCAGTGAAC -3'
(R):5'- CACAGTGGTTTGTTGTTGTTTATTTG -3'

Posted On

2019-11-12