Mutagenetix > Incidental Mutations

Incidental Mutation 'R4992:Sptlc3'

386235

Institutional Source

Beutler Lab

Gene Symbol

Sptlc3

Ensembl Gene

ENSMUSG00000039092

Gene Name

serine palmitoyltransferase, long chain base subunit 3

Synonyms

MMRRC Submission

042586-MU

Accession Numbers

Is this an essential gene?

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

Stock #

R4992 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

139493913-139637674 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

G to A at 139596003 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Valine to Isoleucine at position 406 (V406I)

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: V406I

PolyPhen 2 Score 0.038 (Sensitivity: 0.94; Specificity: 0.82)

SMART Domains

Protein: ENSMUSP00000048313
Gene: ENSMUSG00000039092
AA Change: V406I

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: V406I

PolyPhen 2 Score 0.038 (Sensitivity: 0.94; Specificity: 0.82)

SMART Domains

Protein: ENSMUSP00000105710
Gene: ENSMUSG00000039092
AA Change: V406I

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: 99.2%
3x: 98.5%
10x: 96.8%
20x: 93.7%

Validation Efficiency

98% (84/86)

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: 81 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4930407I10Rik	G	A	15: 82,064,002	R700Q	possibly damaging	Het
4930444P10Rik	T	A	1: 16,080,877	E27V	probably damaging	Het
Acsm4	T	A	7: 119,711,417	I509N	probably benign	Het
Asb18	T	C	1: 89,952,863	M143V	probably benign	Het
Birc6	A	G	17: 74,689,256	D4475G	probably benign	Het
Bsn	A	T	9: 108,115,548	S1002T	probably damaging	Het
Bub3	T	C	7: 131,560,806	S33P	probably damaging	Het
Ccna1	T	A	3: 55,049,890	R35S	probably damaging	Het
Cdc23	T	A	18: 34,646,919	M119L	probably benign	Het
Ces1a	A	G	8: 93,045,022	V49A	probably benign	Het
Chil1	A	T	1: 134,188,626	E282D	probably benign	Het
Crocc	G	A	4: 141,046,666	A220V	probably damaging	Het
Cstf1	A	G	2: 172,377,800	Y277C	probably damaging	Het
D930020B18Rik	C	G	10: 121,654,761	P89A	probably damaging	Het
D930020B18Rik	C	T	10: 121,654,762	P89L	probably damaging	Het
Dennd5a	A	G	7: 109,894,712	S1262P	probably damaging	Het
Dnajb5	G	A	4: 42,953,386		probably null	Het
E330034G19Rik	A	G	14: 24,306,996	K200R	unknown	Het
Ect2l	A	G	10: 18,172,729	F156S	probably benign	Het
Egf	T	C	3: 129,711,530		probably null	Het
Elmo1	T	C	13: 20,342,519	F413S	probably damaging	Het
Elmo3	T	A	8: 105,309,501	Y607*	probably null	Het
Eno3	A	G	11: 70,658,647	D98G	probably damaging	Het
Ephb2	A	G	4: 136,660,839	V651A	probably damaging	Het
Fbp1	C	T	13: 62,865,074	V102I	probably benign	Het
Gcn1l1	T	C	5: 115,599,166	V1321A	probably benign	Het
Gimd1	A	T	3: 132,634,957	Y78F	probably benign	Het
Glmn	T	G	5: 107,557,301	D483A	probably damaging	Het
Gsr	C	T	8: 33,693,913	T401I	probably damaging	Het
Htr3b	G	A	9: 48,959,218	H62Y	possibly damaging	Het
Ifna6	T	C	4: 88,827,540	V42A	probably benign	Het
Igkv4-80	A	C	6: 69,016,665	S81A	probably benign	Het
Inpp4b	A	T	8: 82,033,208	R627S	probably damaging	Het
Kif13a	C	T	13: 46,777,163	V142M	probably damaging	Het
Lims1	A	C	10: 58,410,241		probably benign	Het
Ltn1	T	C	16: 87,405,587	T1059A	possibly damaging	Het
Lyst	T	C	13: 13,661,163	L1810P	probably damaging	Het
Mboat1	T	G	13: 30,202,360	I119R	possibly damaging	Het
Mgat3	T	A	15: 80,212,542	D523E	probably benign	Het
Mphosph9	T	C	5: 124,304,190	E395G	probably damaging	Het
Mtcl1	G	T	17: 66,342,839	P1877Q	probably damaging	Het
Myo6	T	C	9: 80,283,510	V781A	possibly damaging	Het
Ncoa3	T	A	2: 166,069,939	M1395K	probably benign	Het
Nhlrc2	T	A	19: 56,570,534	D150E	probably benign	Het
Nlrp9a	T	C	7: 26,557,386	V54A	probably benign	Het
Olfr392	G	A	11: 73,814,320	T254I	probably damaging	Het
Olfr411	A	G	11: 74,347,197	I129T	probably damaging	Het
Parp14	A	T	16: 35,841,142	C1479S	probably benign	Het
Pdcd1lg2	T	C	19: 29,446,084	V176A	probably damaging	Het
Pibf1	T	A	14: 99,150,667	N416K	probably damaging	Het
Polb	A	T	8: 22,645,071	V115E	probably damaging	Het
Polq	T	A	16: 37,061,162	N1229K	possibly damaging	Het
Ppp1r21	A	T	17: 88,569,080	D440V	probably benign	Het
Ppp2ca	T	A	11: 52,113,206	H63Q	possibly damaging	Het
Prl7a1	C	T	13: 27,635,686		probably null	Het
Rgs1	C	A	1: 144,246,322	K77N	probably damaging	Het
Rnf112	T	A	11: 61,452,711	I100F	possibly damaging	Het
Rnf139	G	T	15: 58,898,476	E117*	probably null	Het
Robo1	G	A	16: 72,979,868	V743I	probably damaging	Het
Scarf1	T	C	11: 75,522,230	L434P	probably damaging	Het
Scarf1	T	C	11: 75,526,015	V761A	probably benign	Het
Sgsm1	A	T	5: 113,282,620	S300T	possibly damaging	Het
Slc26a7	T	G	4: 14,565,508	T192P	probably damaging	Het
Smarcc2	A	G	10: 128,474,710	K403E	probably damaging	Het
Snai3	G	A	8: 122,456,332	T158M	possibly damaging	Het
Spata31d1a	T	C	13: 59,703,151	N388D	probably benign	Het
Tgds	A	C	14: 118,117,763	Y197D	probably damaging	Het
Tll1	G	T	8: 64,093,944	R323S	probably damaging	Het
Tmem55b	A	G	14: 50,929,233	V179A	probably damaging	Het
Trim14	A	G	4: 46,507,110	Y369H	probably damaging	Het
Ube2nl	C	T	7: 61,549,364		noncoding transcript	Het
Ube3a	T	A	7: 59,284,820	D560E	possibly damaging	Het
Vmn2r10	A	G	5: 108,997,726	V505A	possibly damaging	Het
Vmn2r114	T	G	17: 23,291,791	I572L	probably benign	Het
Vmn2r26	A	T	6: 124,026,111	Q160L	probably benign	Het
Vmn2r75	A	C	7: 86,166,167		probably null	Het
Vps8	A	G	16: 21,461,408	K336E	possibly damaging	Het
Zfp324	T	C	7: 12,969,373	S32P	probably benign	Het
Zfp366	T	C	13: 99,229,495	I388T	possibly damaging	Het
Zfp68	A	T	5: 138,607,337	N203K	possibly damaging	Het
Zhx2	A	T	15: 57,823,587	N784I	probably damaging	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
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'- ACCACTGAAGGCTGGTTGTTG -3'
(R):5'- TGTTGTTGAAGACTGCATGTAC -3'

Sequencing Primer
(F):5'- GTCTTTTGAGGACCTAAGCAAATG -3'
(R):5'- GGTGATAGTTCTAGTATGCTCATCAC -3'

Posted On

2016-05-10