Mutagenetix > Incidental Mutation

Incidental Mutation 'R1470:Sptlc2'

165848

Institutional Source

Beutler Lab

Gene Symbol

Sptlc2

Ensembl Gene

ENSMUSG00000021036

Gene Name

serine palmitoyltransferase, long chain base subunit 2

Synonyms

LCB2

MMRRC Submission

039523-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R1470 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

87305058-87388355 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 87355640 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Methionine to Leucine at position 171 (M171L)

Ref Sequence

ENSEMBL: ENSMUSP00000021424 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000021424]

AlphaFold

P97363

Predicted Effect

probably benign
Transcript: ENSMUST00000021424
AA Change: M171L

PolyPhen 2 Score 0.002 (Sensitivity: 0.99; Specificity: 0.30)

SMART Domains

Protein: ENSMUSP00000021424
Gene: ENSMUSG00000021036
AA Change: M171L

Domain	Start	End	E-Value	Type
Pfam:Aminotran_1_2	166	526	7.2e-60	PFAM

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000167911

Meta Mutation Damage Score

0.1116

Coding Region Coverage

1x: 99.7%
3x: 98.4%
10x: 90.6%
20x: 68.6%

Validation Efficiency

MGI Phenotype

FUNCTION: This gene encodes a long chain base subunit of serine palmitoyltransferase. The enzyme, serine palmitoyltransferase, consists of two different subunits, and is the key enzyme in sphingolipid biosynthesis. It catalyzes the pyridoxal-5-prime-phosphate-dependent condensation of L-serine and palmitoyl-CoA to 3-oxosphinganine. A mutant allele of this gene in mice is used as a model for the human disease 'Susceptibilty to Psoriasis 1'. Mutations in the human gene are associated with hereditary sensory neuropathy type I. [provided by RefSeq, Sep 2015]
PHENOTYPE: Mice homozygous for a knock-out allele exhibit embryonic lethality. Mice heterozygous for this allele exhibit abnormal liver and circulating shingolipid levels. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 123 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4932438A13Rik	T	C	3: 36,998,331 (GRCm38)	M3060T	probably benign	Het
Aak1	T	A	6: 86,967,355 (GRCm38)	S749T	unknown	Het
Abcb4	A	T	5: 8,940,968 (GRCm38)	I843F	probably damaging	Het
Actr8	T	A	14: 29,986,969 (GRCm38)	H244Q	possibly damaging	Het
Adgrv1	A	G	13: 81,382,298 (GRCm38)	Y5886H	probably benign	Het
Agk	T	A	6: 40,386,817 (GRCm38)	W244R	probably damaging	Het
Ankrd11	C	A	8: 122,899,724 (GRCm38)	V161L	probably damaging	Het
Arap3	T	C	18: 37,989,196 (GRCm38)		probably null	Het
Armc3	A	G	2: 19,238,736 (GRCm38)	M88V	probably benign	Het
Atp13a5	G	T	16: 29,349,015 (GRCm38)	P109T	probably benign	Het
Avpr1b	T	A	1: 131,600,585 (GRCm38)	V282D	probably damaging	Het
Baz2b	T	C	2: 59,978,546 (GRCm38)	K120E	possibly damaging	Het
Cacng6	G	A	7: 3,424,888 (GRCm38)	C76Y	probably damaging	Het
Cactin	G	T	10: 81,323,151 (GRCm38)	E279*	probably null	Het
Car9	A	G	4: 43,510,222 (GRCm38)	Y268C	probably damaging	Het
Ccdc146	T	A	5: 21,319,566 (GRCm38)	I263F	probably damaging	Het
Cdh16	T	G	8: 104,618,371 (GRCm38)	S429R	probably benign	Het
Cep250	A	G	2: 155,991,075 (GRCm38)	E1639G	probably damaging	Het
Ces1d	A	T	8: 93,195,021 (GRCm38)	V38D	possibly damaging	Het
Chd1	A	T	17: 15,726,283 (GRCm38)	Q97L	possibly damaging	Het
Ciita	G	A	16: 10,514,468 (GRCm38)	D898N	possibly damaging	Het
Clstn1	A	G	4: 149,634,722 (GRCm38)	N336S	possibly damaging	Het
Cntnap5a	A	G	1: 116,259,519 (GRCm38)	D607G	probably damaging	Het
Col1a2	G	A	6: 4,518,822 (GRCm38)		probably benign	Het
Col20a1	C	T	2: 180,994,960 (GRCm38)	H245Y	probably benign	Het
Coq8b	A	T	7: 27,252,309 (GRCm38)	T399S	probably benign	Het
Cpn2	A	G	16: 30,260,185 (GRCm38)	S233P	probably benign	Het
Cryz	G	A	3: 154,606,476 (GRCm38)	G70D	probably damaging	Het
Def6	T	A	17: 28,225,982 (GRCm38)	D451E	possibly damaging	Het
Dnah8	T	A	17: 30,747,277 (GRCm38)	C2480*	probably null	Het
Dnah9	T	C	11: 65,927,822 (GRCm38)	N3230S	probably benign	Het
Dyrk4	G	T	6: 126,916,374 (GRCm38)	S15*	probably null	Het
Erc1	T	C	6: 119,694,602 (GRCm38)	R917G	probably damaging	Het
Frem3	G	T	8: 80,611,191 (GRCm38)	V38L	probably benign	Het
Gas2l3	T	C	10: 89,413,934 (GRCm38)	I441V	probably benign	Het
Gm14393	T	A	2: 175,063,981 (GRCm38)	Y6F	probably damaging	Het
Gm1527	A	G	3: 28,915,268 (GRCm38)	K256E	possibly damaging	Het
Gm21905	G	T	5: 67,946,397 (GRCm38)		probably benign	Het
Gtf2ird1	T	A	5: 134,395,802 (GRCm38)		probably null	Het
Hmces	C	A	6: 87,936,139 (GRCm38)	T292K	probably benign	Het
Hpse2	G	A	19: 43,388,253 (GRCm38)	S20L	probably benign	Het
Ikbke	A	T	1: 131,276,487 (GRCm38)	V23E	probably null	Het
Ino80	A	T	2: 119,379,649 (GRCm38)	V1387E	probably damaging	Het
Islr	G	T	9: 58,157,306 (GRCm38)	A306D	probably damaging	Het
Jakmip1	G	A	5: 37,100,838 (GRCm38)	G276D	probably damaging	Het
Jchain	A	G	5: 88,526,120 (GRCm38)	V55A	probably benign	Het
Kalrn	T	C	16: 34,187,471 (GRCm38)	K1350E	probably damaging	Het
Kansl1l	T	C	1: 66,801,997 (GRCm38)	Q48R	possibly damaging	Het
Kmt5a	T	C	5: 124,447,271 (GRCm38)	L23P	probably damaging	Het
Lrba	C	T	3: 86,737,142 (GRCm38)	H381Y	probably damaging	Het
Lrrc32	T	C	7: 98,499,357 (GRCm38)	V448A	probably benign	Het
Mapkbp1	T	C	2: 120,017,820 (GRCm38)	M617T	probably damaging	Het
Mfap1a	T	C	2: 121,502,801 (GRCm38)	M50V	probably benign	Het
Mgam	G	T	6: 40,759,128 (GRCm38)	A854S	probably damaging	Het
Myo18b	C	A	5: 112,693,033 (GRCm38)	R2298L	probably damaging	Het
Myo1h	T	A	5: 114,319,704 (GRCm38)	M92K	probably damaging	Het
Nlrp2	T	A	7: 5,300,951 (GRCm38)	T192S	probably benign	Het
Nr2f1	A	T	13: 78,198,165 (GRCm38)	Y137N	possibly damaging	Het
Nup98	T	A	7: 102,147,306 (GRCm38)	D841V	probably damaging	Het
Nvl	A	G	1: 181,139,262 (GRCm38)	V59A	probably damaging	Het
Ogdhl	C	A	14: 32,346,788 (GRCm38)	N948K	probably damaging	Het
Olfr530	A	G	7: 140,373,113 (GRCm38)	S166P	probably benign	Het
Olfr538	A	G	7: 140,574,749 (GRCm38)	T199A	probably benign	Het
Olfr578	A	C	7: 102,984,323 (GRCm38)	Y280*	probably null	Het
Olfr743	T	C	14: 50,533,702 (GRCm38)	S97P	possibly damaging	Het
Osgin1	G	A	8: 119,444,965 (GRCm38)	R166H	probably damaging	Het
Palb2	A	T	7: 122,107,523 (GRCm38)	F741I	probably benign	Het
Palb2	G	T	7: 122,107,524 (GRCm38)	Y740*	probably null	Het
Parvb	G	A	15: 84,271,308 (GRCm38)	D65N	probably benign	Het
Parvb	G	A	15: 84,271,252 (GRCm38)	G46D	probably damaging	Het
Pcsk2	A	T	2: 143,546,518 (GRCm38)	K10*	probably null	Het
Pde3a	C	T	6: 141,466,206 (GRCm38)	A502V	probably benign	Het
Pfas	T	C	11: 68,991,359 (GRCm38)	I893V	probably benign	Het
Pla2g4a	A	T	1: 149,840,720 (GRCm38)	D663E	probably damaging	Het
Prickle2	G	A	6: 92,458,602 (GRCm38)	P6L	probably damaging	Het
Prx	T	A	7: 27,517,601 (GRCm38)	M648K	probably benign	Het
Ptpn21	T	C	12: 98,688,476 (GRCm38)	N744S	probably benign	Het
Ptprq	C	T	10: 107,718,574 (GRCm38)	V97M	probably damaging	Het
Pvr	T	C	7: 19,918,624 (GRCm38)	E122G	possibly damaging	Het
Racgap1	T	C	15: 99,639,775 (GRCm38)	K15E	probably damaging	Het
Rock1	C	T	18: 10,136,091 (GRCm38)		probably null	Het
Rorc	T	A	3: 94,397,302 (GRCm38)	Y331*	probably null	Het
Rpl37	T	C	15: 5,118,614 (GRCm38)	V91A	probably benign	Het
Rrp36	T	A	17: 46,672,380 (GRCm38)	K103*	probably null	Het
Ryr3	T	A	2: 112,653,007 (GRCm38)	M4142L	probably benign	Het
Sash1	A	T	10: 8,789,593 (GRCm38)	L125H	probably damaging	Het
Scn5a	T	C	9: 119,536,475 (GRCm38)	M369V	possibly damaging	Het
Sfi1	TCGC	TC	11: 3,146,254 (GRCm38)		probably null	Het
Sfi1	C	CT	11: 3,146,255 (GRCm38)		probably null	Het
Siglec1	A	T	2: 131,070,387 (GRCm38)	N1678K	probably benign	Het
Slc15a5	A	T	6: 138,072,994 (GRCm38)	V141E	probably benign	Het
Slc8a3	A	T	12: 81,199,710 (GRCm38)	H856Q	probably benign	Het
Srcap	T	A	7: 127,559,727 (GRCm38)		probably benign	Het
St6gal2	A	G	17: 55,490,943 (GRCm38)	D310G	probably damaging	Het
Susd2	T	A	10: 75,638,054 (GRCm38)	D689V	probably damaging	Het
Suz12	A	T	11: 80,019,732 (GRCm38)	E303V	possibly damaging	Het
Taldo1	C	A	7: 141,398,587 (GRCm38)	T150K	probably damaging	Het
Tg	T	A	15: 66,849,463 (GRCm38)	F274I	possibly damaging	Het
Tmem151b	T	C	17: 45,545,737 (GRCm38)	D259G	probably damaging	Het
Tmem179	G	T	12: 112,501,854 (GRCm38)	H64Q	probably benign	Het
Tmem236	A	G	2: 14,218,921 (GRCm38)	T174A	probably benign	Het
Tnc	A	T	4: 63,966,574 (GRCm38)	N1821K	probably damaging	Het
Tnfrsf11a	A	G	1: 105,825,048 (GRCm38)	N261S	probably damaging	Het
Trank1	C	A	9: 111,343,232 (GRCm38)	F96L	possibly damaging	Het
Trim56	T	A	5: 137,113,163 (GRCm38)	I500F	probably damaging	Het
Ttc30b	G	T	2: 75,937,811 (GRCm38)	S199R	probably benign	Het
Ttll5	A	G	12: 85,879,394 (GRCm38)	I321V	possibly damaging	Het
Ttn	C	A	2: 76,778,023 (GRCm38)	W17852L	probably damaging	Het
Twnk	G	A	19: 45,009,381 (GRCm38)	V450M	probably damaging	Het
Uba52	A	G	8: 70,509,556 (GRCm38)	I127T	possibly damaging	Het
Ubr4	T	A	4: 139,421,226 (GRCm38)		probably null	Het
Uggt1	A	T	1: 36,176,796 (GRCm38)	M130K	probably benign	Het
Ulk4	T	A	9: 121,081,656 (GRCm38)	T1101S	probably benign	Het
Urb1	A	G	16: 90,752,014 (GRCm38)	S2269P	probably benign	Het
Ush2a	G	T	1: 188,400,206 (GRCm38)	R875L	probably benign	Het
Usp9y	T	A	Y: 1,332,471 (GRCm38)	H1624L	probably benign	Het
Vipr1	T	C	9: 121,665,520 (GRCm38)	L308S	possibly damaging	Het
Xdh	T	G	17: 73,891,112 (GRCm38)	K1260T	probably damaging	Het
Yipf4	A	G	17: 74,493,968 (GRCm38)	I94V	probably benign	Het
Zfhx4	A	G	3: 5,413,146 (GRCm38)	*3582W	probably null	Het
Zfp58	T	C	13: 67,492,025 (GRCm38)	N116D	possibly damaging	Het
Zfp750	C	A	11: 121,511,993 (GRCm38)	R643L	probably benign	Het
Znfx1	A	G	2: 167,042,587 (GRCm38)	V51A	possibly damaging	Het

Other mutations in Sptlc2

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00757:Sptlc2	APN	12	87,369,068 (GRCm38)	missense	probably damaging	0.99
IGL02458:Sptlc2	APN	12	87,309,893 (GRCm38)	utr 3 prime	probably benign
IGL02734:Sptlc2	APN	12	87,355,670 (GRCm38)	missense	probably damaging	0.97
IGL03252:Sptlc2	APN	12	87,355,657 (GRCm38)	missense	probably benign	0.00
lopsided	UTSW	12	87,341,565 (GRCm38)	missense	probably benign	0.27
shinola	UTSW	12	87,350,295 (GRCm38)	missense	possibly damaging	0.64
R0087:Sptlc2	UTSW	12	87,369,118 (GRCm38)	missense	probably benign
R0116:Sptlc2	UTSW	12	87,356,680 (GRCm38)	missense	probably benign	0.00
R0492:Sptlc2	UTSW	12	87,346,806 (GRCm38)	splice site	probably null
R1353:Sptlc2	UTSW	12	87,341,746 (GRCm38)	missense	probably damaging	1.00
R1470:Sptlc2	UTSW	12	87,355,640 (GRCm38)	missense	probably benign	0.00
R3417:Sptlc2	UTSW	12	87,346,808 (GRCm38)	splice site	probably benign
R3735:Sptlc2	UTSW	12	87,341,565 (GRCm38)	missense	probably benign	0.27
R3736:Sptlc2	UTSW	12	87,341,565 (GRCm38)	missense	probably benign	0.27
R4278:Sptlc2	UTSW	12	87,336,151 (GRCm38)	missense	probably benign	0.04
R5252:Sptlc2	UTSW	12	87,336,055 (GRCm38)	missense	possibly damaging	0.49
R5593:Sptlc2	UTSW	12	87,369,083 (GRCm38)	missense	probably benign	0.11
R5656:Sptlc2	UTSW	12	87,346,761 (GRCm38)	missense	probably damaging	1.00
R5801:Sptlc2	UTSW	12	87,341,771 (GRCm38)	splice site	probably null
R6256:Sptlc2	UTSW	12	87,355,531 (GRCm38)	missense	probably damaging	1.00
R6280:Sptlc2	UTSW	12	87,388,131 (GRCm38)	missense	probably benign
R6520:Sptlc2	UTSW	12	87,355,662 (GRCm38)	missense	probably benign
R6808:Sptlc2	UTSW	12	87,350,295 (GRCm38)	missense	possibly damaging	0.64
R7133:Sptlc2	UTSW	12	87,350,377 (GRCm38)	missense	probably benign	0.00
R7274:Sptlc2	UTSW	12	87,341,606 (GRCm38)	missense	probably benign	0.24
R7366:Sptlc2	UTSW	12	87,314,049 (GRCm38)	critical splice donor site	probably null
R7602:Sptlc2	UTSW	12	87,341,689 (GRCm38)	missense	probably damaging	0.99
R9085:Sptlc2	UTSW	12	87,336,065 (GRCm38)	missense	probably benign	0.00
R9710:Sptlc2	UTSW	12	87,312,759 (GRCm38)	missense	probably benign	0.44
Z1177:Sptlc2	UTSW	12	87,369,044 (GRCm38)	missense	probably benign	0.01

Predicted Primers

PCR Primer
(F):5'- ACGCTAACACTGTACCTGCATTACTC -3'
(R):5'- AGTAGTACCAAAGTGCCCTCCAGAAG -3'

Sequencing Primer
(F):5'- TGCATTACTCACTCCTGAGC -3'
(R):5'- AGGACATCTTTAGCTGTCACAC -3'

Posted On

2014-03-28