Mutagenetix > Incidental Mutation

Incidental Mutation 'R5656:Sptlc2'

442345

Institutional Source

Beutler Lab

Gene Symbol

Sptlc2

Ensembl Gene

ENSMUSG00000021036

Gene Name

serine palmitoyltransferase, long chain base subunit 2

Synonyms

LCB2, Spt2

MMRRC Submission

043302-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R5656 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

87351832-87435129 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to T at 87393535 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Leucine to Glutamine at position 264 (L264Q)

Ref Sequence

ENSEMBL: ENSMUSP00000021424 (fasta)

Gene Model

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

AlphaFold

P97363

Predicted Effect

probably damaging
Transcript: ENSMUST00000021424
AA Change: L264Q

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000021424
Gene: ENSMUSG00000021036
AA Change: L264Q

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

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000167911

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000169845

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000170110

Coding Region Coverage

1x: 99.2%
3x: 98.5%
10x: 97.1%
20x: 94.9%

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: 60 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4933405L10Rik	A	G	8: 106,436,144 (GRCm39)	S139G	probably benign	Het
Adrb3	T	C	8: 27,717,405 (GRCm39)	D348G	probably damaging	Het
Atg2b	A	G	12: 105,587,587 (GRCm39)	V1959A	probably benign	Het
Bicral	G	A	17: 47,119,295 (GRCm39)	T742M	probably damaging	Het
Bub1b	T	A	2: 118,435,912 (GRCm39)	I60N	probably damaging	Het
Ccdc162	A	G	10: 41,445,930 (GRCm39)	V414A	probably benign	Het
Cd22	T	G	7: 30,569,198 (GRCm39)	Y612S	probably damaging	Het
Cd68	T	A	11: 69,555,247 (GRCm39)	I320F	probably damaging	Het
Clca3a2	A	T	3: 144,503,393 (GRCm39)	N852K	probably benign	Het
Cpa6	T	A	1: 10,399,739 (GRCm39)	H363L	probably benign	Het
Ddx18	A	T	1: 121,489,087 (GRCm39)	L320Q	probably damaging	Het
Dnah5	A	G	15: 28,421,210 (GRCm39)	D3849G	probably benign	Het
Eci1	T	A	17: 24,656,283 (GRCm39)	N164K	probably damaging	Het
Efs	T	C	14: 55,154,584 (GRCm39)	T552A	probably damaging	Het
Fbp1	C	A	13: 63,023,010 (GRCm39)	V96L	probably damaging	Het
Gtf3c1	T	A	7: 125,261,826 (GRCm39)	N1139I	probably benign	Het
Gucy1b2	T	C	14: 62,660,430 (GRCm39)	Y152C	probably damaging	Het
Gxylt1	A	T	15: 93,143,542 (GRCm39)	L362Q	probably damaging	Het
Iqcd	A	G	5: 120,743,191 (GRCm39)		probably null	Het
Klhl41	T	A	2: 69,513,876 (GRCm39)	I585N	possibly damaging	Het
Map6	A	G	7: 98,985,505 (GRCm39)	K470E	probably damaging	Het
Mast3	T	C	8: 71,238,865 (GRCm39)	T496A	probably damaging	Het
Mbd6	A	T	10: 127,121,155 (GRCm39)		probably benign	Het
Melk	A	G	4: 44,312,237 (GRCm39)	K183R	possibly damaging	Het
Mta1	T	C	12: 113,086,759 (GRCm39)	V152A	probably damaging	Het
Naa35	G	A	13: 59,770,680 (GRCm39)		probably benign	Het
Nav3	A	C	10: 109,600,494 (GRCm39)	S1378A	probably damaging	Het
Ncapd3	T	A	9: 26,962,941 (GRCm39)	D415E	possibly damaging	Het
Nlrp4f	G	A	13: 65,338,685 (GRCm39)	R651*	probably null	Het
Or1e1f	T	A	11: 73,855,536 (GRCm39)	M34K	probably damaging	Het
Or5b121	A	G	19: 13,507,744 (GRCm39)	T280A	probably benign	Het
Or5p72	A	G	7: 108,021,825 (GRCm39)	I16V	probably benign	Het
P2rx7	A	T	5: 122,811,780 (GRCm39)	R364W	probably damaging	Het
Phactr2	T	C	10: 13,264,447 (GRCm39)	D2G	probably benign	Het
Phc3	G	T	3: 31,020,015 (GRCm39)	S28R	probably damaging	Het
Ppfia1	A	T	7: 144,073,711 (GRCm39)		probably null	Het
Prdm10	C	T	9: 31,264,713 (GRCm39)	T667M	probably benign	Het
Pwwp2b	T	A	7: 138,835,887 (GRCm39)	S443T	possibly damaging	Het
Pzp	T	C	6: 128,467,035 (GRCm39)	T1113A	probably damaging	Het
Rapgef6	A	G	11: 54,526,962 (GRCm39)	E551G	possibly damaging	Het
Sec23ip	A	G	7: 128,378,508 (GRCm39)	Y774C	probably damaging	Het
Setdb2	T	C	14: 59,656,567 (GRCm39)	D266G	probably damaging	Het
Shank1	T	C	7: 44,002,310 (GRCm39)	V1343A	probably benign	Het
Slf2	T	A	19: 44,961,674 (GRCm39)	D1064E	probably benign	Het
Slu7	A	G	11: 43,334,245 (GRCm39)	K424E	probably benign	Het
Smg1	A	T	7: 117,753,887 (GRCm39)		probably benign	Het
Sra1	A	G	18: 36,811,460 (GRCm39)	S93P	probably damaging	Het
Sult1c2	T	C	17: 54,271,680 (GRCm39)	E169G	probably benign	Het
Sv2a	A	G	3: 96,092,888 (GRCm39)	D196G	probably damaging	Het
Tbc1d22b	A	G	17: 29,813,754 (GRCm39)	I362M	probably damaging	Het
Tenm3	T	C	8: 48,681,797 (GRCm39)	D2611G	probably damaging	Het
Tmem43	T	C	6: 91,457,690 (GRCm39)	F191L	probably benign	Het
Trbv13-2	T	A	6: 41,098,628 (GRCm39)	Y68N	probably benign	Het
Ttn	T	G	2: 76,604,998 (GRCm39)	D18312A	possibly damaging	Het
Ublcp1	A	G	11: 44,356,433 (GRCm39)	V95A	probably damaging	Het
Usp17ld	A	G	7: 102,900,047 (GRCm39)	V295A	probably damaging	Het
Vmn1r29	T	A	6: 58,285,152 (GRCm39)	L291M	possibly damaging	Het
Vsig10l	C	T	7: 43,113,575 (GRCm39)	R176*	probably null	Het
Zbtb46	A	G	2: 181,065,210 (GRCm39)		probably null	Het
Zfp644	A	G	5: 106,785,848 (GRCm39)	V233A	probably benign	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
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
R7602:Sptlc2	UTSW	12	87,388,463 (GRCm39)	missense	probably damaging	0.99
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'- TTAAAAGTCAAATCAAGGAAGACAGT -3'
(R):5'- TGGATAATTAAGTTGGCCAGGTGA -3'

Sequencing Primer
(F):5'- TTCGACCTCCCAAGTACTAGAATTG -3'
(R):5'- TTGGCCAGGTGAAGAAACTGTC -3'

Posted On

2016-11-09