Mutagenetix > Incidental Mutation

Incidental Mutation 'R9582:Lypla1'

722579

Institutional Source

Beutler Lab

Gene Symbol

Lypla1

Ensembl Gene

ENSMUSG00000025903

Gene Name

lysophospholipase 1

Synonyms

Pla1a, Gm39587

MMRRC Submission

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R9582 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

4878046-4916958 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

C to T at 4911248 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Proline to Serine at position 178 (P178S)

Ref Sequence

ENSEMBL: ENSMUSP00000027036 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000027036] [ENSMUST00000115529] [ENSMUST00000119612] [ENSMUST00000131119] [ENSMUST00000134384] [ENSMUST00000137887] [ENSMUST00000150971] [ENSMUST00000155020]

AlphaFold

P97823

Predicted Effect

probably benign
Transcript: ENSMUST00000027036
AA Change: P178S

PolyPhen 2 Score 0.433 (Sensitivity: 0.89; Specificity: 0.90)

SMART Domains

Protein: ENSMUSP00000027036
Gene: ENSMUSG00000025903
AA Change: P178S

Domain	Start	End	E-Value	Type
Pfam:Abhydrolase_2	8	226	2.5e-92	PFAM
Pfam:Abhydrolase_5	23	209	4.3e-14	PFAM
Pfam:Abhydrolase_3	82	170	2.6e-7	PFAM

Predicted Effect

possibly damaging
Transcript: ENSMUST00000115529
AA Change: P144S

PolyPhen 2 Score 0.492 (Sensitivity: 0.88; Specificity: 0.90)

SMART Domains

Protein: ENSMUSP00000111191
Gene: ENSMUSG00000025903
AA Change: P144S

Domain	Start	End	E-Value	Type
Pfam:Abhydrolase_2	8	125	1.5e-49	PFAM
Pfam:Abhydrolase_2	122	192	2.2e-20	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000119612

SMART Domains

Protein: ENSMUSP00000137647
Gene: ENSMUSG00000025903

Domain	Start	End	E-Value	Type
Pfam:Abhydrolase_2	8	92	1.1e-33	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000131119
AA Change: P120S

PolyPhen 2 Score 0.433 (Sensitivity: 0.89; Specificity: 0.90)

SMART Domains

Protein: ENSMUSP00000118453
Gene: ENSMUSG00000025903
AA Change: P120S

Domain	Start	End	E-Value	Type
Pfam:Abhydrolase_2	1	142	8.1e-56	PFAM
Pfam:Abhydrolase_5	10	141	7.8e-11	PFAM
Pfam:Abhydrolase_6	11	139	9.2e-8	PFAM
Pfam:Abhydrolase_3	20	139	4e-8	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000134384
AA Change: P178S

PolyPhen 2 Score 0.258 (Sensitivity: 0.91; Specificity: 0.88)

SMART Domains

Protein: ENSMUSP00000137104
Gene: ENSMUSG00000025903
AA Change: P178S

Domain	Start	End	E-Value	Type
Pfam:Abhydrolase_2	8	224	5.6e-85	PFAM
Pfam:Abhydrolase_5	23	209	4e-14	PFAM
Pfam:Abhydrolase_6	24	160	2.5e-10	PFAM
Pfam:Abhydrolase_3	85	195	2.4e-7	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000137887

SMART Domains

Protein: ENSMUSP00000119456
Gene: ENSMUSG00000025903

Domain	Start	End	E-Value	Type
Pfam:Abhydrolase_2	8	142	5.6e-48	PFAM
Pfam:Abhydrolase_5	23	141	9.3e-10	PFAM
Pfam:Abhydrolase_6	24	141	7.2e-12	PFAM
Pfam:Abhydrolase_3	62	140	2.1e-7	PFAM

Predicted Effect

possibly damaging
Transcript: ENSMUST00000150971
AA Change: P178S

PolyPhen 2 Score 0.943 (Sensitivity: 0.80; Specificity: 0.95)

SMART Domains

Protein: ENSMUSP00000137248
Gene: ENSMUSG00000025903
AA Change: P178S

Domain	Start	End	E-Value	Type
Pfam:Abhydrolase_2	8	215	1.3e-84	PFAM
Pfam:Abhydrolase_5	23	209	4.4e-14	PFAM
Pfam:Abhydrolase_6	24	160	3.6e-10	PFAM
Pfam:Abhydrolase_3	85	195	1.1e-7	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000155020

SMART Domains

Protein: ENSMUSP00000136108
Gene: ENSMUSG00000104217

Domain	Start	End	E-Value	Type
low complexity region	8	24	N/A	INTRINSIC

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.7%
20x: 99.1%

Validation Efficiency

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a member of the alpha/beta hydrolase superfamily. The encoded protein functions as a homodimer, exhibiting both depalmitoylating as well as lysophospholipase activity, and may be involved in Ras localization and signaling. Alternate splicing results in multiple transcript variants. Pseudogenes of this gene have been defined on chromosomes 4, 6, and 7. [provided by RefSeq, Jul 2013]

Allele List at MGI

Other mutations in this stock

Total: 52 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1110002E22Rik	T	A	3: 137,772,766 (GRCm39)	F652I	probably damaging	Het
Adam17	A	T	12: 21,386,665 (GRCm39)	I457K	probably benign	Het
Arpin	T	C	7: 79,585,038 (GRCm39)		probably benign	Het
Bhlhe40	A	G	6: 108,638,467 (GRCm39)	E51G	probably benign	Het
Ces1a	C	T	8: 93,766,156 (GRCm39)	D153N	probably benign	Het
Cog7	T	C	7: 121,536,200 (GRCm39)	M547V	probably benign	Het
Csrnp2	C	T	15: 100,386,067 (GRCm39)	R57K	possibly damaging	Het
Dact1	A	T	12: 71,365,619 (GRCm39)	K763M	probably damaging	Het
Ddost	A	T	4: 138,035,583 (GRCm39)	I101F	possibly damaging	Het
Dyrk1b	C	T	7: 27,882,028 (GRCm39)	R130W	probably damaging	Het
Ep400	A	C	5: 110,824,315 (GRCm39)		probably null	Het
Fam227a	A	G	15: 79,501,978 (GRCm39)	V532A	probably benign	Het
Flnc	C	A	6: 29,460,736 (GRCm39)	T2609K	probably damaging	Het
Gbp10	A	G	5: 105,372,256 (GRCm39)	V168A	probably benign	Het
Gp5	A	G	16: 30,127,057 (GRCm39)	V539A	probably benign	Het
H2-T13	T	A	17: 36,392,375 (GRCm39)	R33S	unknown	Het
Itih5	A	G	2: 10,195,013 (GRCm39)	E135G	probably benign	Het
L2hgdh	A	G	12: 69,739,172 (GRCm39)	V433A	probably benign	Het
Leng9	A	G	7: 4,152,263 (GRCm39)	S138P	probably damaging	Het
Ltbp2	G	A	12: 84,837,864 (GRCm39)	P1192L	probably benign	Het
Ly6g6e	T	C	17: 35,296,159 (GRCm39)	V10A	probably benign	Het
Mark1	A	G	1: 184,651,858 (GRCm39)	F216L	possibly damaging	Het
Mertk	G	A	2: 128,624,527 (GRCm39)	R646Q	possibly damaging	Het
Mmp9	A	C	2: 164,791,235 (GRCm39)	D135A	probably benign	Het
Nefl	A	G	14: 68,324,849 (GRCm39)	K529E	unknown	Het
Nicn1	C	T	9: 108,171,708 (GRCm39)	R163C	possibly damaging	Het
Nwd1	A	G	8: 73,421,917 (GRCm39)	T988A	probably damaging	Het
P4ha2	T	A	11: 54,022,065 (GRCm39)	C529*	probably null	Het
Pcdhb4	T	A	18: 37,441,417 (GRCm39)	F242L	probably damaging	Het
Pced1b	A	G	15: 97,282,450 (GRCm39)	N163S	probably damaging	Het
Pde8b	A	G	13: 95,169,369 (GRCm39)	V585A	probably damaging	Het
Pknox2	T	A	9: 36,804,252 (GRCm39)	T432S	probably damaging	Het
Rad18	A	G	6: 112,658,298 (GRCm39)		probably null	Het
Rpgrip1l	C	T	8: 91,996,886 (GRCm39)	V665I	probably benign	Het
Rreb1	A	G	13: 38,114,734 (GRCm39)	I698V	probably benign	Het
Schip1	TCTGGCC	TC	3: 68,525,060 (GRCm39)		probably null	Het
Slc2a4	C	T	11: 69,837,450 (GRCm39)	V32M	probably damaging	Het
Slc40a1	A	G	1: 45,950,499 (GRCm39)	Y318H	probably damaging	Het
Spag16	A	G	1: 69,897,717 (GRCm39)	T156A	probably benign	Het
Srebf1	C	A	11: 60,097,868 (GRCm39)	A103S	probably benign	Het
Sspn	C	T	6: 145,899,334 (GRCm39)		probably benign	Het
Stoml2	A	T	4: 43,030,238 (GRCm39)		probably null	Het
Stra6	T	A	9: 58,054,770 (GRCm39)	V319E	probably damaging	Het
Syt7	T	C	19: 10,416,780 (GRCm39)	F414L	probably damaging	Het
Tet3	G	T	6: 83,381,226 (GRCm39)	P314Q	probably damaging	Het
Tnrc18	A	T	5: 142,757,128 (GRCm39)	L1313Q		Het
Topors	A	T	4: 40,260,460 (GRCm39)	D941E	unknown	Het
Txnip	T	A	3: 96,465,659 (GRCm39)	C36*	probably null	Het
Uba3	A	T	6: 97,168,491 (GRCm39)	M178K	probably damaging	Het
Vmn1r6	A	G	6: 56,979,925 (GRCm39)	T196A	probably benign	Het
Vwc2	T	A	11: 11,066,129 (GRCm39)	S72R	probably benign	Het
Wnk2	A	G	13: 49,210,975 (GRCm39)	S1627P	probably benign	Het

Other mutations in Lypla1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00501:Lypla1	APN	1	4,898,810 (GRCm39)	missense	probably damaging	1.00
IGL01571:Lypla1	APN	1	4,915,211 (GRCm39)	missense	probably benign	0.15
IGL01592:Lypla1	APN	1	4,898,874 (GRCm39)	critical splice donor site	probably null
IGL01865:Lypla1	APN	1	4,907,259 (GRCm39)	missense	probably damaging	0.96
IGL02442:Lypla1	APN	1	4,902,610 (GRCm39)	splice site	probably benign
IGL03005:Lypla1	APN	1	4,902,613 (GRCm39)	splice site	probably benign
R0095:Lypla1	UTSW	1	4,900,550 (GRCm39)	splice site	probably benign
R2278:Lypla1	UTSW	1	4,911,321 (GRCm39)	splice site	probably null
R3766:Lypla1	UTSW	1	4,911,201 (GRCm39)	missense	probably benign	0.04
R5805:Lypla1	UTSW	1	4,900,517 (GRCm39)	missense	possibly damaging	0.54
R6014:Lypla1	UTSW	1	4,878,594 (GRCm39)	splice site	probably null
R6027:Lypla1	UTSW	1	4,907,299 (GRCm39)	critical splice donor site	probably null
R6842:Lypla1	UTSW	1	4,902,563 (GRCm39)	missense	probably benign	0.14
R7285:Lypla1	UTSW	1	4,911,321 (GRCm39)	missense	probably benign
R7564:Lypla1	UTSW	1	4,878,590 (GRCm39)	critical splice donor site	probably null
R9105:Lypla1	UTSW	1	4,911,282 (GRCm39)	missense	probably damaging	1.00
R9496:Lypla1	UTSW	1	4,898,813 (GRCm39)	start gained	probably benign

Predicted Primers

PCR Primer
(F):5'- GTACTTTGCCAAGACATTTGACTG -3'
(R):5'- TGCTCATTTGTAAAAGGCGATCAG -3'

Sequencing Primer
(F):5'- GCCAAGACATTTGACTGAATTATGAG -3'
(R):5'- ATGAGCTGTGCATCATGC -3'

Posted On

2022-08-09