Mutagenetix > Incidental Mutations

Incidental Mutation 'R4601:Sptlc3'

345601

Institutional Source

Beutler Lab

Gene Symbol

Sptlc3

Ensembl Gene

ENSMUSG00000039092

Gene Name

serine palmitoyltransferase, long chain base subunit 3

Synonyms

Accession Numbers

Is this an essential gene?

Probably non essential (E-score: 0.093) question?

Stock #

R4601 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

139493913-139637674 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

G to A at 139636680 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Valine to Isoleucine at position 520 (V520I)

Ref Sequence

ENSEMBL: ENSMUSP00000105710 (fasta)

Gene Model

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

AlphaFold

Q8BG54

Predicted Effect

probably benign
Transcript: ENSMUST00000047370
AA Change: V520I

PolyPhen 2 Score 0.006 (Sensitivity: 0.97; Specificity: 0.75)

SMART Domains

Protein: ENSMUSP00000048313
Gene: ENSMUSG00000039092
AA Change: V520I

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

probably benign
Transcript: ENSMUST00000110083
AA Change: V520I

PolyPhen 2 Score 0.006 (Sensitivity: 0.97; Specificity: 0.75)

SMART Domains

Protein: ENSMUSP00000105710
Gene: ENSMUSG00000039092
AA Change: V520I

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

noncoding transcript
Transcript: ENSMUST00000134801

Meta Mutation Damage Score

0.0898

Coding Region Coverage

1x: 99.3%
3x: 98.7%
10x: 97.1%
20x: 94.5%

Validation Efficiency

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: 91 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1700029J07Rik	A	T	8: 45,970,468	I69N	probably damaging	Het
4930435E12Rik	A	G	16: 38,828,018	V243A	probably benign	Het
Aars2	T	A	17: 45,516,921	D555E	probably damaging	Het
Abca16	T	G	7: 120,436,697	F334L	probably damaging	Het
Abcc4	T	A	14: 118,632,163	M186L	probably benign	Het
Agap3	T	C	5: 24,476,408	L120P	probably damaging	Het
Ak7	G	A	12: 105,713,575	V123M	probably benign	Het
Aldh1a7	A	T	19: 20,715,979	V192D	probably damaging	Het
Ankrd36	A	G	11: 5,570,102	D59G	probably benign	Het
Arsi	G	A	18: 60,916,651	G202E	probably benign	Het
Cacna1e	A	G	1: 154,471,613	V936A	probably benign	Het
Camkv	T	C	9: 107,946,096	V107A	probably damaging	Het
Camp	T	C	9: 109,848,662	E80G	probably damaging	Het
Ccdc66	T	C	14: 27,500,420	N122S	probably damaging	Het
Cd101	G	A	3: 100,993,888	T960M	possibly damaging	Het
Cdk18	A	G	1: 132,116,919	V323A	possibly damaging	Het
Celf2	G	T	2: 6,586,020	N279K	possibly damaging	Het
Cemip	T	C	7: 83,951,618	I932V	probably damaging	Het
Cep250	C	A	2: 155,962,053	Q28K	probably benign	Het
Ces2f	T	C	8: 104,949,964	C97R	probably damaging	Het
Cfap126	G	T	1: 171,114,058	G41C	possibly damaging	Het
Chat	T	C	14: 32,424,155	M354V	probably benign	Het
Clca4b	A	T	3: 144,927,184	D168E	possibly damaging	Het
Cpxm1	T	A	2: 130,393,576	M499L	possibly damaging	Het
Dennd3	T	A	15: 73,567,160	W1126R	probably damaging	Het
Dgkb	T	C	12: 38,602,820	S735P	probably damaging	Het
Dlec1	T	C	9: 119,147,134		probably null	Het
Dnajc6	T	C	4: 101,611,264	F166L	probably damaging	Het
Dph5	A	G	3: 115,899,777	N115D	possibly damaging	Het
Ercc3	G	A	18: 32,245,571	A202T	probably benign	Het
Erich3	A	T	3: 154,764,738	D136V	unknown	Het
Exoc2	T	C	13: 30,882,268	N475S	probably benign	Het
Fam160a1	T	C	3: 85,741,180	M26V	probably damaging	Het
Fam217a	T	C	13: 34,911,302	D310G	probably damaging	Het
Fam53a	C	T	5: 33,600,663	S372N	probably benign	Het
Fbn2	C	G	18: 58,053,733	G1699R	probably damaging	Het
Fbxo46	T	C	7: 19,135,564	V36A	probably benign	Het
G6pc	A	G	11: 101,372,741	Y127C	probably damaging	Het
Gba2	A	G	4: 43,573,810	F161L	probably damaging	Het
Gif	A	C	19: 11,752,190	D171A	probably damaging	Het
Gja1	T	C	10: 56,388,229	L228P	probably damaging	Het
Gm20834	A	G	Y: 10,323,178	V86A	probably benign	Het
Hmcn1	A	T	1: 150,738,645	C1337S	probably damaging	Het
Il1rl1	T	A	1: 40,441,300	S30T	possibly damaging	Het
Itgb4	A	G	11: 116,005,722	T1436A	probably damaging	Het
Itk	T	A	11: 46,336,515	Q427L	probably benign	Het
Klhdc4	T	C	8: 121,799,527	E291G	probably damaging	Het
Map4	T	A	9: 110,052,819	S250R	possibly damaging	Het
Mnt	T	A	11: 74,836,459	V57E	possibly damaging	Het
Mrc2	G	A	11: 105,348,431		probably null	Het
Mslnl	G	A	17: 25,742,934	V128M	probably damaging	Het
Musk	A	T	4: 58,301,625	I128F	probably damaging	Het
Myh4	G	A	11: 67,250,310	A733T	possibly damaging	Het
Myo5a	T	A	9: 75,136,388	F220I	probably damaging	Het
Npas3	A	G	12: 54,044,578	H305R	probably damaging	Het
Nrcam	A	T	12: 44,591,056	Y1132F	probably damaging	Het
Nt5c3b	A	C	11: 100,432,918	D189E	probably benign	Het
Nuf2	A	G	1: 169,506,114	L331P	probably damaging	Het
Nup214	C	T	2: 31,997,965	T646I	probably benign	Het
Olfr112	T	C	17: 37,564,185	N42S	probably damaging	Het
Pcdh18	T	C	3: 49,744,725	E1096G	probably damaging	Het
Pgm1	T	A	5: 64,107,727	F364I	probably benign	Het
Pikfyve	A	G	1: 65,234,262	N612S	probably damaging	Het
Pla2g4e	T	G	2: 120,186,382	H226P	possibly damaging	Het
Ppp3cb	T	C	14: 20,520,646	N339S	possibly damaging	Het
Prkd2	G	T	7: 16,843,648		probably benign	Het
Rnf133	T	C	6: 23,649,042	E296G	possibly damaging	Het
Sav1	A	T	12: 69,984,321	D142E	probably benign	Het
Scn3b	C	A	9: 40,288,423	P212T	probably damaging	Het
Sel1l	A	T	12: 91,833,053		probably null	Het
Sept9	A	G	11: 117,360,484	K543E	probably damaging	Het
Serpinb12	T	A	1: 106,949,153	D66E	probably benign	Het
Slc35e2	T	C	4: 155,617,649	F290S	probably benign	Het
Snrpa	A	G	7: 27,195,533	M1T	probably null	Het
Soga1	T	C	2: 157,039,924	K736R	probably benign	Het
Srpk3	A	G	X: 73,774,941	H79R	possibly damaging	Het
Stox2	A	G	8: 47,192,935	S497P	probably damaging	Het
Stradb	G	A	1: 58,993,572	S361N	probably damaging	Het
Sult3a2	T	C	10: 33,782,087	K10R	probably benign	Het
Susd4	A	G	1: 182,858,460	N192D	probably damaging	Het
Tcp10a	T	A	17: 7,325,975	D32E	probably benign	Het
Tdpoz4	T	A	3: 93,797,032	V212D	probably damaging	Het
Tdrd5	T	A	1: 156,284,374	T479S	probably benign	Het
Tex10	T	C	4: 48,452,946	D671G	probably benign	Het
Traj37	T	C	14: 54,181,539		probably benign	Het
Ttc7b	G	A	12: 100,500,117	R79C	probably damaging	Het
Vmn2r115	T	A	17: 23,346,399	L420Q	probably benign	Het
Wdr24	T	A	17: 25,828,207		probably null	Het
Wdr81	T	A	11: 75,445,658	Q516L	probably damaging	Het
Zfp516	A	G	18: 82,956,039	T121A	probably benign	Het
Zmat1	A	T	X: 134,972,945	S566T	probably damaging	Homo

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
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
R7733:Sptlc3	UTSW	2	139631368	missense	possibly damaging	0.77
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'- ACACTCACAATGTTGAGTTAGAGC -3'
(R):5'- TGAAATTGTCCTCAGAAGGGG -3'

Sequencing Primer
(F):5'- ATTACTGGAGCATACTGGCC -3'
(R):5'- TTGTCCTCAGAAGGGGTAAAATAC -3'

Posted On

2015-09-25