Mutagenetix > Incidental Mutation

Incidental Mutation 'R7602:Sptlc2'

588079

Institutional Source

Beutler Lab

Gene Symbol

Sptlc2

Ensembl Gene

ENSMUSG00000021036

Gene Name

serine palmitoyltransferase, long chain base subunit 2

Synonyms

LCB2, Spt2

MMRRC Submission

045674-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R7602 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

87351832-87435129 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 87388463 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Tyrosine to Histidine at position 340 (Y340H)

Ref Sequence

ENSEMBL: ENSMUSP00000021424 (fasta)

Gene Model

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

AlphaFold

P97363

Predicted Effect

probably damaging
Transcript: ENSMUST00000021424
AA Change: Y340H

PolyPhen 2 Score 0.991 (Sensitivity: 0.71; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000021424
Gene: ENSMUSG00000021036
AA Change: Y340H

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

Meta Mutation Damage Score

0.8793

Coding Region Coverage

1x: 100.0%
3x: 100.0%
10x: 99.8%
20x: 99.2%

Validation Efficiency

100% (58/58)

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: 59 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1700025G04Rik	A	T	1: 151,856,266 (GRCm39)	Y34N	probably damaging	Het
A2m	T	C	6: 121,618,966 (GRCm39)	V237A	probably damaging	Het
A2m	A	T	6: 121,647,895 (GRCm39)	D1129V	possibly damaging	Het
Aadacl2fm3	T	C	3: 59,784,697 (GRCm39)	I390T	probably benign	Het
Abca7	A	G	10: 79,833,846 (GRCm39)		probably null	Het
Adam34l	C	T	8: 44,079,703 (GRCm39)	G174R	probably damaging	Het
Ap3m2	T	C	8: 23,282,770 (GRCm39)	N256S	probably benign	Het
Atr	C	T	9: 95,789,436 (GRCm39)	H1531Y	possibly damaging	Het
Carmil3	C	T	14: 55,738,965 (GRCm39)	A873V	probably null	Het
Casp8	A	C	1: 58,872,898 (GRCm39)	K258T	probably benign	Het
Cast	A	G	13: 74,885,084 (GRCm39)	S222P	probably benign	Het
Cpsf7	C	T	19: 10,512,737 (GRCm39)	P274S	probably damaging	Het
Ddx24	A	T	12: 103,382,519 (GRCm39)	L688*	probably null	Het
Ddx59	A	G	1: 136,361,559 (GRCm39)	I475V	probably benign	Het
Dhx29	T	A	13: 113,081,093 (GRCm39)	S376T	possibly damaging	Het
Dhx57	G	T	17: 80,582,290 (GRCm39)	N438K	probably benign	Het
Dlk1	T	A	12: 109,421,551 (GRCm39)		probably null	Het
Efcab15	T	C	11: 103,091,004 (GRCm39)	M114V	probably benign	Het
Epha6	T	C	16: 59,595,931 (GRCm39)	D920G	probably damaging	Het
Exo5	A	T	4: 120,778,818 (GRCm39)	V349E	probably benign	Het
Fam234b	T	C	6: 135,202,241 (GRCm39)	V321A	possibly damaging	Het
Gbp3	A	G	3: 142,274,822 (GRCm39)	E383G	probably benign	Het
Gga2	T	C	7: 121,596,553 (GRCm39)	N408S	probably benign	Het
Gse1	T	C	8: 121,296,043 (GRCm39)	V532A	unknown	Het
Hnrnpul2	T	C	19: 8,808,673 (GRCm39)	Y712H	probably damaging	Het
Hpca	T	C	4: 129,014,019 (GRCm39)		probably benign	Het
Ifitm3	A	G	7: 140,590,372 (GRCm39)	F63L	probably damaging	Het
Inava	G	T	1: 136,153,135 (GRCm39)	C252*	probably null	Het
Kank1	A	T	19: 25,399,525 (GRCm39)	T940S	probably benign	Het
Klhl9	C	A	4: 88,640,646 (GRCm39)		probably benign	Het
Krt36	T	C	11: 99,993,786 (GRCm39)	M351V	probably benign	Het
Mthfd2	T	C	6: 83,288,830 (GRCm39)	N125D	probably benign	Het
Muc4	C	G	16: 32,575,221 (GRCm39)	Q1269E	probably benign	Het
Ncoa2	A	G	1: 13,247,350 (GRCm39)	S358P	possibly damaging	Het
Nmnat1	T	C	4: 149,557,808 (GRCm39)	H78R	probably benign	Het
Or10s1	T	G	9: 39,986,455 (GRCm39)	L288R	probably damaging	Het
Or5k1	T	C	16: 58,617,343 (GRCm39)	I289V	possibly damaging	Het
Or5m13b	A	T	2: 85,754,146 (GRCm39)	Y178F	probably damaging	Het
Or9r3	A	G	10: 129,948,179 (GRCm39)	M160T	probably benign	Het
Pabpc4	A	T	4: 123,186,685 (GRCm39)	D302V	possibly damaging	Het
Pgap1	A	T	1: 54,582,345 (GRCm39)	S167R	probably damaging	Het
Phf12	T	C	11: 77,914,109 (GRCm39)	L517P	probably benign	Het
Rcan2	A	G	17: 44,328,689 (GRCm39)	D86G	probably benign	Het
Ryk	T	C	9: 102,775,715 (GRCm39)	Y442H	probably damaging	Het
Scfd2	G	T	5: 74,623,271 (GRCm39)	Q421K	probably benign	Het
Sirpa	G	T	2: 129,451,072 (GRCm39)	V111F	probably damaging	Het
Skint4	A	T	4: 111,975,468 (GRCm39)	T143S	possibly damaging	Het
Slc12a8	C	A	16: 33,445,494 (GRCm39)	H463N	probably benign	Het
Sp110	G	A	1: 85,506,813 (GRCm39)	R417C	probably benign	Het
Ssc5d	T	A	7: 4,945,745 (GRCm39)	W926R	possibly damaging	Het
Tgfa	A	G	6: 86,246,944 (GRCm39)	E82G	probably damaging	Het
Thrsp	A	G	7: 97,066,514 (GRCm39)	I66T	probably damaging	Het
Ttn	T	C	2: 76,681,988 (GRCm39)	E1003G	unknown	Het
Tube1	A	T	10: 39,018,262 (GRCm39)	H113L	probably benign	Het
Uri1	A	G	7: 37,681,053 (GRCm39)	V117A	probably benign	Het
Ush2a	G	A	1: 188,380,606 (GRCm39)	C2305Y	probably damaging	Het
Zbtb7a	T	G	10: 80,980,010 (GRCm39)	V68G	probably damaging	Het
Zfr	T	A	15: 12,159,763 (GRCm39)	D686E	possibly damaging	Het
Zscan4f	G	A	7: 11,135,308 (GRCm39)	S238N	possibly damaging	Het

Other mutations in Sptlc2

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00757:Sptlc2	APN	12	87,415,842 (GRCm39)	missense	probably damaging	0.99
IGL02458:Sptlc2	APN	12	87,356,667 (GRCm39)	utr 3 prime	probably benign
IGL02734:Sptlc2	APN	12	87,402,444 (GRCm39)	missense	probably damaging	0.97
IGL03252:Sptlc2	APN	12	87,402,431 (GRCm39)	missense	probably benign	0.00
lopsided	UTSW	12	87,388,339 (GRCm39)	missense	probably benign	0.27
shinola	UTSW	12	87,397,069 (GRCm39)	missense	possibly damaging	0.64
R0087:Sptlc2	UTSW	12	87,415,892 (GRCm39)	missense	probably benign
R0116:Sptlc2	UTSW	12	87,403,454 (GRCm39)	missense	probably benign	0.00
R0492:Sptlc2	UTSW	12	87,393,580 (GRCm39)	splice site	probably null
R1353:Sptlc2	UTSW	12	87,388,520 (GRCm39)	missense	probably damaging	1.00
R1470:Sptlc2	UTSW	12	87,402,414 (GRCm39)	missense	probably benign	0.00
R1470:Sptlc2	UTSW	12	87,402,414 (GRCm39)	missense	probably benign	0.00
R3417:Sptlc2	UTSW	12	87,393,582 (GRCm39)	splice site	probably benign
R3735:Sptlc2	UTSW	12	87,388,339 (GRCm39)	missense	probably benign	0.27
R3736:Sptlc2	UTSW	12	87,388,339 (GRCm39)	missense	probably benign	0.27
R4278:Sptlc2	UTSW	12	87,382,925 (GRCm39)	missense	probably benign	0.04
R5252:Sptlc2	UTSW	12	87,382,829 (GRCm39)	missense	possibly damaging	0.49
R5593:Sptlc2	UTSW	12	87,415,857 (GRCm39)	missense	probably benign	0.11
R5656:Sptlc2	UTSW	12	87,393,535 (GRCm39)	missense	probably damaging	1.00
R5801:Sptlc2	UTSW	12	87,388,545 (GRCm39)	splice site	probably null
R6256:Sptlc2	UTSW	12	87,402,305 (GRCm39)	missense	probably damaging	1.00
R6280:Sptlc2	UTSW	12	87,434,905 (GRCm39)	missense	probably benign
R6520:Sptlc2	UTSW	12	87,402,436 (GRCm39)	missense	probably benign
R6808:Sptlc2	UTSW	12	87,397,069 (GRCm39)	missense	possibly damaging	0.64
R7133:Sptlc2	UTSW	12	87,397,151 (GRCm39)	missense	probably benign	0.00
R7274:Sptlc2	UTSW	12	87,388,380 (GRCm39)	missense	probably benign	0.24
R7366:Sptlc2	UTSW	12	87,360,823 (GRCm39)	critical splice donor site	probably null
R9085:Sptlc2	UTSW	12	87,382,839 (GRCm39)	missense	probably benign	0.00
R9710:Sptlc2	UTSW	12	87,359,533 (GRCm39)	missense	probably benign	0.44
Z1177:Sptlc2	UTSW	12	87,415,818 (GRCm39)	missense	probably benign	0.01

Predicted Primers

PCR Primer
(F):5'- TTGGCGAGCGAGTCTAAAG -3'
(R):5'- CAAGGCATTCATAATGAGCATAGAG -3'

Sequencing Primer
(F):5'- GAGCGAGTCTAAAGGCCTATTTTACC -3'
(R):5'- AGAGTGCTTTCCTGGCATATTCAAG -3'

Posted On

2019-10-24