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

C130053K05Rik

MMRRC Submission

045789-MU

Accession Numbers

Essential gene?

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

Stock #

R7733 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

139335833-139478981 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

G to T at 139473288 bp (GRCm39)

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: 133,271,240 (GRCm39)	S95T	probably benign	Het
Abca8a	A	G	11: 109,945,413 (GRCm39)	F1070L	probably benign	Het
Acsl3	G	C	1: 78,665,953 (GRCm39)		probably null	Het
Adarb2	T	A	13: 8,802,644 (GRCm39)	S640T	possibly damaging	Het
Adgre5	T	C	8: 84,456,025 (GRCm39)	D257G	probably benign	Het
Adora2b	A	T	11: 62,156,165 (GRCm39)	I205F	possibly damaging	Het
Asb14	A	G	14: 26,634,309 (GRCm39)	M505V	probably benign	Het
Atrnl1	T	C	19: 57,690,420 (GRCm39)	V876A	probably benign	Het
AU040320	A	G	4: 126,729,322 (GRCm39)	N495D	possibly damaging	Het
Bcam	A	T	7: 19,494,313 (GRCm39)	V361E	probably benign	Het
Ccdc7a	T	A	8: 129,719,533 (GRCm39)	E247V	probably damaging	Het
Cd84	T	A	1: 171,668,226 (GRCm39)	M1K	probably null	Het
Cfap43	C	T	19: 47,886,432 (GRCm39)	R61H	possibly damaging	Het
Clec4a1	A	G	6: 122,909,109 (GRCm39)	D159G	possibly damaging	Het
Ctcfl	C	T	2: 172,958,985 (GRCm39)	R247Q	probably benign	Het
Ctdnep1	G	A	11: 69,880,835 (GRCm39)	R236Q	probably damaging	Het
Cwf19l2	A	T	9: 3,450,066 (GRCm39)	H589L	probably benign	Het
Cyp2u1	G	T	3: 131,096,676 (GRCm39)	A34E	probably benign	Het
Cyp4x1	A	G	4: 114,977,391 (GRCm39)	S281P	possibly damaging	Het
Dag1	T	C	9: 108,086,047 (GRCm39)	T365A	probably benign	Het
Dhx57	A	T	17: 80,572,503 (GRCm39)		probably null	Het
Dnajb1	T	G	8: 84,335,006 (GRCm39)	S16A	probably benign	Het
Dsc2	A	T	18: 20,181,372 (GRCm39)	L145Q	probably benign	Het
Dsc2	G	C	18: 20,181,373 (GRCm39)	L145V	probably benign	Het
Eefsec	T	C	6: 88,353,202 (GRCm39)	T156A	possibly damaging	Het
Eif6	T	A	2: 155,665,152 (GRCm39)	D169V	probably benign	Het
Ell3	C	A	2: 121,273,001 (GRCm39)	G3V	possibly damaging	Het
Eprs1	A	T	1: 185,129,358 (GRCm39)	H615L	probably benign	Het
Fbxw10	A	G	11: 62,764,223 (GRCm39)	Y630C	unknown	Het
Fcgbpl1	A	T	7: 27,839,390 (GRCm39)	D401V	probably damaging	Het
G6pc2	C	T	2: 69,050,527 (GRCm39)	Q51*	probably null	Het
Glt8d1	C	T	14: 30,723,935 (GRCm39)		probably benign	Het
Gpr4	T	C	7: 18,956,635 (GRCm39)	Y186H	probably damaging	Het
Grhpr	T	C	4: 44,981,494 (GRCm39)		probably benign	Het
Gsdma3	A	G	11: 98,526,041 (GRCm39)	H264R	probably damaging	Het
Hcfc2	A	G	10: 82,575,013 (GRCm39)	Y224C	probably benign	Het
Helz2	A	G	2: 180,872,148 (GRCm39)	F2608S	possibly damaging	Het
Herc2	C	T	7: 55,838,412 (GRCm39)	T3313M	probably damaging	Het
Hmgcl	A	T	4: 135,687,394 (GRCm39)	H223L	probably benign	Het
Igf2r	A	G	17: 12,958,256 (GRCm39)	V139A	possibly damaging	Het
Iqcn	A	G	8: 71,170,100 (GRCm39)	T1397A	possibly damaging	Het
Kif5a	T	A	10: 127,072,609 (GRCm39)	T727S	probably benign	Het
Kifc1	G	A	17: 34,102,543 (GRCm39)	R357W	probably damaging	Het
Krt81	T	A	15: 101,361,395 (GRCm39)	S62C	probably damaging	Het
Lgi2	T	C	5: 52,695,873 (GRCm39)	N362S	probably benign	Het
Lig1	G	T	7: 13,030,157 (GRCm39)	R378L	possibly damaging	Het
Map3k13	C	T	16: 21,740,436 (GRCm39)	R588C	probably damaging	Het
Mov10l1	T	A	15: 88,909,004 (GRCm39)	F1008L	probably damaging	Het
Nr4a2	A	G	2: 57,002,333 (GRCm39)	V40A	probably benign	Het
Nrde2	A	T	12: 100,110,399 (GRCm39)	C206S	possibly damaging	Het
Or4f14d	C	T	2: 111,960,386 (GRCm39)	V257I	probably benign	Het
Parp1	T	C	1: 180,427,777 (GRCm39)		probably null	Het
Pcdhb12	A	G	18: 37,570,089 (GRCm39)	T412A	probably damaging	Het
Plekhh2	T	A	17: 84,890,952 (GRCm39)	Y839*	probably null	Het
Pnpla6	T	A	8: 3,572,660 (GRCm39)	F316I	probably benign	Het
Prcp	C	T	7: 92,550,506 (GRCm39)	T101M	probably damaging	Het
Prex2	G	T	1: 11,252,183 (GRCm39)	R1076L	probably benign	Het
Prpf40b	T	C	15: 99,206,224 (GRCm39)		probably null	Het
Psd3	T	G	8: 68,573,568 (GRCm39)	K204N	possibly damaging	Het
Ptpro	C	A	6: 137,391,284 (GRCm39)	C801*	probably null	Het
Ptprt	A	G	2: 161,417,707 (GRCm39)	V923A	probably damaging	Het
Ptprz1	T	A	6: 23,000,383 (GRCm39)	D824E	probably benign	Het
Rasgrf1	A	G	9: 89,863,780 (GRCm39)	D582G	probably benign	Het
Rfc2	T	C	5: 134,622,070 (GRCm39)	L183P	probably damaging	Het
Rnf114	T	C	2: 167,354,438 (GRCm39)	V173A	probably damaging	Het
Scn3a	T	A	2: 65,338,994 (GRCm39)	I562F	probably benign	Het
Setmar	T	C	6: 108,053,088 (GRCm39)	I194T	probably damaging	Het
Sptb	A	T	12: 76,644,695 (GRCm39)		probably null	Het
Sptbn2	C	G	19: 4,799,040 (GRCm39)	R2037G	probably benign	Het
Svep1	C	A	4: 58,049,239 (GRCm39)	A3423S	probably benign	Het
Sycp1	T	C	3: 102,803,278 (GRCm39)	T511A	probably benign	Het
Synm	T	A	7: 67,385,693 (GRCm39)		probably null	Het
Tada1	C	T	1: 166,217,511 (GRCm39)	P216L	probably damaging	Het
Tas2r117	T	A	6: 132,780,138 (GRCm39)	M92K	probably benign	Het
Thoc2l	T	C	5: 104,667,826 (GRCm39)	F783L	possibly damaging	Het
Thsd1	T	C	8: 22,748,737 (GRCm39)	L536P	probably damaging	Het
Timp2	T	G	11: 118,208,355 (GRCm39)		probably null	Het
Trak1	T	A	9: 121,196,291 (GRCm39)	V41D	possibly damaging	Het
Ubqln3	T	A	7: 103,790,283 (GRCm39)	L602F	probably damaging	Het
Vmn2r59	A	G	7: 41,661,443 (GRCm39)	F791L	probably benign	Het
Wbp4	A	G	14: 79,714,480 (GRCm39)		probably null	Het
Zng1	T	C	19: 24,918,158 (GRCm39)	D204G	probably damaging	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
R7412:Sptlc3	UTSW	2	139,431,537 (GRCm39)	missense	possibly damaging	0.75
R7516:Sptlc3	UTSW	2	139,431,438 (GRCm39)	missense	probably benign	0.11
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'- CAGCAGGATAATTCTATCTTCCCTC -3'
(R):5'- GGATATTGCTGACATACCACAGTG -3'

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

Posted On

2019-11-12