Mutagenetix > Incidental Mutation

Incidental Mutation 'R7412:Sptlc3'

575125

Institutional Source

Beutler Lab

Gene Symbol

Sptlc3

Ensembl Gene

ENSMUSG00000039092

Gene Name

serine palmitoyltransferase, long chain base subunit 3

Synonyms

C130053K05Rik

MMRRC Submission

045493-MU

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.122) question?

Stock #

R7412 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

139335833-139478981 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 139431537 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Glutamic Acid to Glycine at position 353 (E353G)

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: E353G

PolyPhen 2 Score 0.755 (Sensitivity: 0.85; Specificity: 0.92)

SMART Domains

Protein: ENSMUSP00000048313
Gene: ENSMUSG00000039092
AA Change: E353G

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: E353G

PolyPhen 2 Score 0.755 (Sensitivity: 0.85; Specificity: 0.92)

SMART Domains

Protein: ENSMUSP00000105710
Gene: ENSMUSG00000039092
AA Change: E353G

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

Coding Region Coverage

1x: 100.0%
3x: 100.0%
10x: 99.7%
20x: 99.1%

Validation Efficiency

97% (71/73)

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: 75 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1700017N19Rik	T	A	10: 100,448,691 (GRCm39)	Y335*	probably null	Het
Alpk1	A	T	3: 127,466,143 (GRCm39)	L1121Q	probably damaging	Het
Alpk1	A	G	3: 127,489,382 (GRCm39)	I99T	probably damaging	Het
Ap2a2	T	A	7: 141,206,049 (GRCm39)	F717I	probably damaging	Het
Arhgap33	C	T	7: 30,222,477 (GRCm39)	D1152N	probably benign	Het
Arvcf	A	G	16: 18,220,350 (GRCm39)	D642G	probably benign	Het
Astn1	T	G	1: 158,329,919 (GRCm39)	M258R	probably damaging	Het
Brinp3	C	G	1: 146,777,748 (GRCm39)	L732V	possibly damaging	Het
Carmil1	T	C	13: 24,282,793 (GRCm39)	D547G	possibly damaging	Het
Ccdc177	A	G	12: 80,805,792 (GRCm39)	F161L	possibly damaging	Het
Cfap57	C	T	4: 118,472,128 (GRCm39)	V84I	probably benign	Het
Cnot10	A	G	9: 114,454,971 (GRCm39)	Y221H	probably damaging	Het
Col6a3	T	A	1: 90,755,855 (GRCm39)	I145F	probably damaging	Het
Crybg2	A	G	4: 133,801,434 (GRCm39)	T865A	probably benign	Het
Cyp4f37	A	G	17: 32,848,818 (GRCm39)	S229G	possibly damaging	Het
Ddx56	G	A	11: 6,211,720 (GRCm39)	T462I	probably damaging	Het
Dhx30	T	C	9: 109,921,966 (GRCm39)	M239V	probably benign	Het
Dusp9	TAAAGCGGAGGCCAAAGCGGAGGCCAAAGCGGAGGCTAAAGCGGAGGCCAAAGCGGAGGCCAAAGCGGAGGCCAAAGCGGAGGCTAAAGCGGAGGCCAAAGCGGAGGCCAAAG	TAAAGCGGAGGCCAAAGCGGAGGCCAAAGCGGAGGCTAAAGCGGAGGCCAAAGCGGAGGCCAAAG	X: 72,684,217 (GRCm39)		probably benign	Het
Enpp5	G	A	17: 44,396,155 (GRCm39)	G356S	probably damaging	Het
Ephb6	A	G	6: 41,597,173 (GRCm39)	K994E	probably damaging	Het
Fam83a	A	C	15: 57,849,821 (GRCm39)	T122P	probably benign	Het
Fbxo24	C	A	5: 137,617,885 (GRCm39)	C293F	possibly damaging	Het
Fech	A	T	18: 64,591,255 (GRCm39)	S390T	probably benign	Het
Fras1	A	G	5: 96,762,748 (GRCm39)	H750R	probably benign	Het
Frmpd2	A	G	14: 33,293,926 (GRCm39)	D1364G	probably benign	Het
Ganab	T	C	19: 8,889,892 (GRCm39)	I652T	probably benign	Het
Gm21103	T	A	14: 17,482,943 (GRCm39)	T153S	probably benign	Het
Gm21886	GGGCCTGCAGACAGTAGGTGCTCACTGAGGCCTGCAGTTAGTAGGTGCTCACTGAGGCCTGCAGACAGTAGGTACTCACTGAGGCCTGCAGACAGTAGGTGCTCACTGAGGCCTGCAGACAGTAGGTGCTCACTGAGGCCTGCAGACAGTAGGTGCTCACTGAGACCTGCAGACAGTAGGTGCTCACTGAG	GGGCCTGCAGACAGTAGGTACTCACTGAGGCCTGCAGACAGTAGGTGCTCACTGAGGCCTGCAGACAGTAGGTGCTCACTGAGGCCTGCAGACAGTAGGTGCTCACTGAGACCTGCAGACAGTAGGTGCTCACTGAG	18: 80,132,967 (GRCm39)		probably benign	Het
Gm5799	A	G	14: 43,781,995 (GRCm39)	I56V	possibly damaging	Het
Gm7276	T	C	18: 77,273,183 (GRCm39)	R184G	unknown	Het
Gmip	T	G	8: 70,273,149 (GRCm39)	D845E	probably benign	Het
Hspa9	T	C	18: 35,082,082 (GRCm39)	K175E	probably damaging	Het
Ipo13	A	G	4: 117,752,068 (GRCm39)	F890L	probably benign	Het
Irag1	A	T	7: 110,522,963 (GRCm39)	V160D	probably benign	Het
Klrb1f	C	T	6: 129,033,308 (GRCm39)	R179*	probably null	Het
Nasp	A	G	4: 116,467,785 (GRCm39)	V400A	possibly damaging	Het
Ncoa7	T	A	10: 30,598,847 (GRCm39)	K25N	possibly damaging	Het
Ndrg1	A	C	15: 66,832,382 (GRCm39)	M1R	probably null	Het
Nf1	G	A	11: 79,364,240 (GRCm39)	A1557T	probably damaging	Het
Nrde2	G	A	12: 100,108,509 (GRCm39)	Q361*	probably null	Het
Opn1sw	A	T	6: 29,379,856 (GRCm39)	L126Q	probably damaging	Het
Or10ak16	A	T	4: 118,750,327 (GRCm39)	I16F	possibly damaging	Het
Or1af1	C	T	2: 37,109,774 (GRCm39)	T91I	possibly damaging	Het
Or1j4	T	C	2: 36,740,478 (GRCm39)	L140P	probably benign	Het
Or5au1	A	T	14: 52,273,310 (GRCm39)	L86*	probably null	Het
Or7g17	A	T	9: 18,768,085 (GRCm39)	I46F	possibly damaging	Het
Or8g50	T	C	9: 39,648,422 (GRCm39)	F104L	probably benign	Het
Osmr	A	G	15: 6,853,048 (GRCm39)	Y616H	probably damaging	Het
Pagr1a	T	C	7: 126,615,736 (GRCm39)	T120A	probably benign	Het
Patj	A	G	4: 98,299,376 (GRCm39)	E166G	probably damaging	Het
Plk4	G	A	3: 40,766,613 (GRCm39)	V764I	probably benign	Het
Polr3h	G	A	15: 81,800,602 (GRCm39)		probably null	Het
Ptprb	T	A	10: 116,177,043 (GRCm39)	D989E	probably benign	Het
Sdk2	A	T	11: 113,758,909 (GRCm39)		probably null	Het
Setd1b	C	A	5: 123,290,639 (GRCm39)	R869S	unknown	Het
Sgcz	T	C	8: 37,990,565 (GRCm39)	I263V	probably benign	Het
Skint8	G	A	4: 111,785,758 (GRCm39)	G68D	probably benign	Het
Slc22a7	A	T	17: 46,745,553 (GRCm39)	V326E	probably benign	Het
Slc39a1	T	G	3: 90,156,396 (GRCm39)	L38R	probably damaging	Het
Slc4a4	A	G	5: 89,362,506 (GRCm39)		probably null	Het
Ssh2	G	T	11: 77,340,934 (GRCm39)	L695F	probably damaging	Het
Tacr2	C	A	10: 62,097,427 (GRCm39)	Y302*	probably null	Het
Tas2r117	T	C	6: 132,780,192 (GRCm39)	L110P	probably damaging	Het
Tex9	A	T	9: 72,394,060 (GRCm39)		probably null	Het
Tmem17	A	T	11: 22,468,645 (GRCm39)	T195S	probably benign	Het
Trcg1	T	A	9: 57,148,766 (GRCm39)	S113T	probably benign	Het
Trpa1	A	T	1: 14,954,422 (GRCm39)	F826I	probably benign	Het
Usp17lc	A	G	7: 103,067,575 (GRCm39)	Y290C	probably damaging	Het
Vmn2r32	T	A	7: 7,477,212 (GRCm39)	D393V	possibly damaging	Het
Wdfy4	A	G	14: 32,871,541 (GRCm39)	L290P		Het
Xpnpep1	G	C	19: 52,994,722 (GRCm39)	A302G	probably benign	Het
Xrn2	T	C	2: 146,891,266 (GRCm39)	L692P	probably damaging	Het
Zgrf1	A	G	3: 127,356,720 (GRCm39)	S649G	probably benign	Het
Zscan4b	C	T	7: 10,634,791 (GRCm39)	C484Y	probably damaging	Het
Zscan4b	T	C	7: 10,635,820 (GRCm39)	D169G	probably benign	Het

Other mutations in Sptlc3

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01392:Sptlc3	APN	2	139,388,341 (GRCm39)	missense	possibly damaging	0.55
IGL01537:Sptlc3	APN	2	139,431,615 (GRCm39)	missense	possibly damaging	0.95
IGL01996:Sptlc3	APN	2	139,423,424 (GRCm39)	splice site	probably benign
IGL02512:Sptlc3	APN	2	139,389,123 (GRCm39)	missense	probably damaging	1.00
IGL03278:Sptlc3	APN	2	139,431,579 (GRCm39)	missense	probably damaging	1.00
IGL03286:Sptlc3	APN	2	139,431,579 (GRCm39)	missense	probably damaging	1.00
R0266:Sptlc3	UTSW	2	139,437,957 (GRCm39)	missense	possibly damaging	0.93
R0362:Sptlc3	UTSW	2	139,388,475 (GRCm39)	splice site	probably benign
R1464:Sptlc3	UTSW	2	139,389,154 (GRCm39)	missense	probably benign	0.00
R1464:Sptlc3	UTSW	2	139,389,154 (GRCm39)	missense	probably benign	0.00
R1494:Sptlc3	UTSW	2	139,431,480 (GRCm39)	missense	possibly damaging	0.58
R1847:Sptlc3	UTSW	2	139,467,843 (GRCm39)	missense	probably benign	0.08
R1919:Sptlc3	UTSW	2	139,408,595 (GRCm39)	missense	possibly damaging	0.66
R2093:Sptlc3	UTSW	2	139,467,794 (GRCm39)	missense	possibly damaging	0.89
R2396:Sptlc3	UTSW	2	139,408,506 (GRCm39)	missense	probably benign	0.44
R2972:Sptlc3	UTSW	2	139,431,581 (GRCm39)	missense	probably damaging	1.00
R2973:Sptlc3	UTSW	2	139,431,581 (GRCm39)	missense	probably damaging	1.00
R2974:Sptlc3	UTSW	2	139,431,581 (GRCm39)	missense	probably damaging	1.00
R4601:Sptlc3	UTSW	2	139,478,600 (GRCm39)	missense	probably benign	0.01
R4602:Sptlc3	UTSW	2	139,478,600 (GRCm39)	missense	probably benign	0.01
R4610:Sptlc3	UTSW	2	139,478,600 (GRCm39)	missense	probably benign	0.01
R4745:Sptlc3	UTSW	2	139,389,087 (GRCm39)	missense	probably damaging	1.00
R4779:Sptlc3	UTSW	2	139,431,509 (GRCm39)	missense	probably benign	0.04
R4992:Sptlc3	UTSW	2	139,437,923 (GRCm39)	missense	probably benign	0.04
R5162:Sptlc3	UTSW	2	139,473,263 (GRCm39)	missense	probably benign	0.11
R5401:Sptlc3	UTSW	2	139,478,643 (GRCm39)	missense	possibly damaging	0.75
R5406:Sptlc3	UTSW	2	139,388,398 (GRCm39)	missense	probably benign	0.26
R5642:Sptlc3	UTSW	2	139,388,328 (GRCm39)	missense	probably damaging	0.96
R5840:Sptlc3	UTSW	2	139,389,126 (GRCm39)	missense	probably damaging	1.00
R6057:Sptlc3	UTSW	2	139,423,533 (GRCm39)	missense	probably damaging	0.99
R6376:Sptlc3	UTSW	2	139,478,692 (GRCm39)	missense	probably benign	0.21
R6852:Sptlc3	UTSW	2	139,408,506 (GRCm39)	missense	probably benign	0.44
R7026:Sptlc3	UTSW	2	139,379,608 (GRCm39)	missense	probably benign
R7516:Sptlc3	UTSW	2	139,431,438 (GRCm39)	missense	probably benign	0.11
R7733:Sptlc3	UTSW	2	139,473,288 (GRCm39)	missense	possibly damaging	0.77
R7826:Sptlc3	UTSW	2	139,389,115 (GRCm39)	missense	probably benign	0.44
R7949:Sptlc3	UTSW	2	139,467,795 (GRCm39)	missense	possibly damaging	0.81
R9224:Sptlc3	UTSW	2	139,336,154 (GRCm39)	missense	probably benign	0.17
R9237:Sptlc3	UTSW	2	139,408,605 (GRCm39)	missense	probably benign	0.40
R9319:Sptlc3	UTSW	2	139,478,730 (GRCm39)	missense	possibly damaging	0.65
R9330:Sptlc3	UTSW	2	139,388,423 (GRCm39)	missense	probably benign

Predicted Primers

PCR Primer
(F):5'- TGCGCTGGAAGGACACTAAC -3'
(R):5'- CACGTGAGCTGAACTGAAAC -3'

Sequencing Primer
(F):5'- GGACACTAACGGAGCTTTCCAG -3'
(R):5'- CTGAAACAGACATGAACTTCAGG -3'

Posted On

2019-10-07