Mutagenetix > Incidental Mutation

Incidental Mutation 'R6906:Lypd1'

538761

Institutional Source

Beutler Lab

Gene Symbol

Lypd1

Ensembl Gene

ENSMUSG00000026344

Gene Name

Ly6/Plaur domain containing 1

Synonyms

C530008O16Rik, 2700050C12Rik, Lynx2

MMRRC Submission

044998-MU

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.060) question?

Stock #

R6906 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

125795359-125840838 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 125838196 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Glutamic Acid to Glycine at position 41 (E41G)

Ref Sequence

ENSEMBL: ENSMUSP00000125149 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000027582] [ENSMUST00000057846] [ENSMUST00000094609] [ENSMUST00000094610] [ENSMUST00000112583] [ENSMUST00000159417] [ENSMUST00000159529] [ENSMUST00000161361] [ENSMUST00000161954] [ENSMUST00000162877] [ENSMUST00000162899]

AlphaFold

Q8BLC3

Predicted Effect

probably benign
Transcript: ENSMUST00000027582

SMART Domains

Protein: ENSMUSP00000027582
Gene: ENSMUSG00000026344

Domain	Start	End	E-Value	Type
LU	24	122	5.18e-2	SMART
low complexity region	126	142	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000057846

SMART Domains

Protein: ENSMUSP00000062229
Gene: ENSMUSG00000049690

Domain	Start	End	E-Value	Type
low complexity region	2	25	N/A	INTRINSIC
coiled coil region	108	186	N/A	INTRINSIC
low complexity region	321	332	N/A	INTRINSIC
low complexity region	755	771	N/A	INTRINSIC
low complexity region	950	971	N/A	INTRINSIC
low complexity region	1070	1085	N/A	INTRINSIC
low complexity region	1181	1200	N/A	INTRINSIC
Pfam:NCKAP5	1298	1602	1.8e-120	PFAM
low complexity region	1728	1742	N/A	INTRINSIC
low complexity region	1757	1771	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000094609

SMART Domains

Protein: ENSMUSP00000092192
Gene: ENSMUSG00000049690

Domain	Start	End	E-Value	Type
low complexity region	70	93	N/A	INTRINSIC
Pfam:NCKAP5	113	364	3.6e-36	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000094610

SMART Domains

Protein: ENSMUSP00000092193
Gene: ENSMUSG00000049690

Domain	Start	End	E-Value	Type
Pfam:NCKAP5	1	101	8.8e-42	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000112583

SMART Domains

Protein: ENSMUSP00000108202
Gene: ENSMUSG00000049690

Domain	Start	End	E-Value	Type
low complexity region	70	93	N/A	INTRINSIC
coiled coil region	176	254	N/A	INTRINSIC
low complexity region	301	324	N/A	INTRINSIC
low complexity region	453	464	N/A	INTRINSIC
low complexity region	887	903	N/A	INTRINSIC
low complexity region	1082	1103	N/A	INTRINSIC
low complexity region	1202	1217	N/A	INTRINSIC
low complexity region	1313	1332	N/A	INTRINSIC
Pfam:NCKAP5	1431	1733	5.3e-119	PFAM
low complexity region	1860	1874	N/A	INTRINSIC
low complexity region	1889	1903	N/A	INTRINSIC

Predicted Effect

probably damaging
Transcript: ENSMUST00000159417
AA Change: E41G

PolyPhen 2 Score 0.992 (Sensitivity: 0.70; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000125149
Gene: ENSMUSG00000026344
AA Change: E41G

Domain	Start	End	E-Value	Type
signal peptide	1	20	N/A	INTRINSIC
LU	23	121	2.5e-4	SMART
low complexity region	125	140	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000159529

SMART Domains

Protein: ENSMUSP00000123824
Gene: ENSMUSG00000026344

Domain	Start	End	E-Value	Type
Blast:LU	1	69	4e-32	BLAST
low complexity region	73	89	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000161361

Predicted Effect

probably benign
Transcript: ENSMUST00000161954

SMART Domains

Protein: ENSMUSP00000125624
Gene: ENSMUSG00000049690

Domain	Start	End	E-Value	Type
low complexity region	2	25	N/A	INTRINSIC
coiled coil region	108	186	N/A	INTRINSIC
low complexity region	233	256	N/A	INTRINSIC
low complexity region	385	396	N/A	INTRINSIC
low complexity region	819	835	N/A	INTRINSIC
low complexity region	1014	1035	N/A	INTRINSIC
low complexity region	1134	1149	N/A	INTRINSIC
low complexity region	1245	1264	N/A	INTRINSIC
Pfam:NCKAP5	1362	1666	2.1e-120	PFAM
low complexity region	1792	1806	N/A	INTRINSIC
low complexity region	1821	1835	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000162877

SMART Domains

Protein: ENSMUSP00000124748
Gene: ENSMUSG00000049690

Domain	Start	End	E-Value	Type
Pfam:NCKAP5	9	296	6e-36	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000162899

SMART Domains

Protein: ENSMUSP00000125158
Gene: ENSMUSG00000026344

Domain	Start	End	E-Value	Type
Blast:LU	1	69	4e-32	BLAST
low complexity region	73	89	N/A	INTRINSIC

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.2%
20x: 97.3%

Validation Efficiency

98% (45/46)

MGI Phenotype

PHENOTYPE: Mice homozygous for a null allele exhibit increased fear and anxiety behaviors with increased spontaneous excitatory postsynaptic current following nicotine treatment. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 46 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abcf2	A	G	5: 24,773,840 (GRCm39)	F350L	possibly damaging	Het
Ahnak2	T	A	12: 112,748,933 (GRCm39)	T305S	probably benign	Het
Anp32a	A	G	9: 62,284,851 (GRCm39)		probably benign	Het
Aplf	A	G	6: 87,607,068 (GRCm39)	S449P	possibly damaging	Het
Arl6ip4	A	G	5: 124,254,614 (GRCm39)	R36G	possibly damaging	Het
Ascc1	G	A	10: 59,840,674 (GRCm39)	D12N	probably benign	Het
Bin1	C	A	18: 32,554,978 (GRCm39)	H243Q	probably benign	Het
Ccdc168	C	T	1: 44,095,173 (GRCm39)	S1975N	probably benign	Het
Ccdc7a	C	A	8: 129,662,162 (GRCm39)	V547L	unknown	Het
Cntnap5c	T	A	17: 58,702,302 (GRCm39)	N1207K	probably benign	Het
Coro7	C	A	16: 4,451,168 (GRCm39)	R507L	probably benign	Het
Crtap	T	A	9: 114,210,700 (GRCm39)	K291N	probably benign	Het
Csmd3	T	C	15: 47,710,569 (GRCm39)	T1569A	probably benign	Het
Dmrta1	A	G	4: 89,580,203 (GRCm39)	T388A	probably benign	Het
Ehd3	T	C	17: 74,137,333 (GRCm39)	F501L	probably damaging	Het
Fbn2	A	C	18: 58,204,891 (GRCm39)	L1184R	possibly damaging	Het
Fhip1b	G	A	7: 105,037,476 (GRCm39)	T369I	probably damaging	Het
Hsf1	T	C	15: 76,361,919 (GRCm39)		probably null	Het
Hycc1	A	T	5: 24,204,956 (GRCm39)	W12R	probably damaging	Het
Kansl1l	T	C	1: 66,762,437 (GRCm39)	H810R	possibly damaging	Het
Lrp5	A	T	19: 3,672,638 (GRCm39)	I557N	probably damaging	Het
Mgam	A	G	6: 40,724,853 (GRCm39)	Y443C	probably damaging	Het
Muc2	A	G	7: 141,284,976 (GRCm39)	D871G	probably damaging	Het
Nup85	T	A	11: 115,471,769 (GRCm39)	Y198N	probably damaging	Het
Obscn	T	A	11: 58,923,744 (GRCm39)	M6578L	possibly damaging	Het
Or8h7	T	C	2: 86,721,091 (GRCm39)	T143A	probably benign	Het
Osbpl5	G	C	7: 143,248,065 (GRCm39)	Q667E	probably damaging	Het
Ovgp1	T	A	3: 105,894,189 (GRCm39)		probably benign	Het
Prl8a2	T	A	13: 27,532,900 (GRCm39)	N37K	probably benign	Het
Ptprf	A	T	4: 118,126,474 (GRCm39)	I93N	possibly damaging	Het
Rnf112	T	C	11: 61,341,215 (GRCm39)	S457G	probably null	Het
Sema3e	A	G	5: 14,290,601 (GRCm39)	D562G	probably damaging	Het
Sesn3	A	G	9: 14,236,937 (GRCm39)	M472V	probably damaging	Het
Sfpq	GCCGCCGCAGCAGCCTCCGCCGCAGCAGCC	GCCGCCGCAGCAGCC	4: 126,915,419 (GRCm39)		probably benign	Het
Shc3	T	C	13: 51,620,595 (GRCm39)	T144A	probably damaging	Het
Sis	A	G	3: 72,826,818 (GRCm39)	L1287P	probably damaging	Het
Srrm2	C	T	17: 24,039,337 (GRCm39)	P2090S	probably damaging	Het
Syne2	T	G	12: 76,042,760 (GRCm39)	D3910E	possibly damaging	Het
Tcaim	C	T	9: 122,663,839 (GRCm39)	T443I	probably benign	Het
Tex19.1	T	C	11: 121,037,948 (GRCm39)	V102A	probably benign	Het
Tpd52l1	T	G	10: 31,208,950 (GRCm39)	T168P	possibly damaging	Het
Trdn	G	A	10: 33,109,944 (GRCm39)	C294Y	probably benign	Het
Trmt1l	T	C	1: 151,327,926 (GRCm39)	Y479H	probably benign	Het
Vmn1r171	G	A	7: 23,331,804 (GRCm39)	V10I	probably benign	Het
Zbtb41	T	A	1: 139,351,128 (GRCm39)	D80E	possibly damaging	Het
Zcchc4	A	G	5: 52,980,976 (GRCm39)	K473E	possibly damaging	Het

Other mutations in Lypd1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
H8562:Lypd1	UTSW	1	125,838,274 (GRCm39)	splice site	probably benign
R0015:Lypd1	UTSW	1	125,838,175 (GRCm39)	missense	possibly damaging	0.59
R0537:Lypd1	UTSW	1	125,840,604 (GRCm39)	unclassified	probably benign
R1838:Lypd1	UTSW	1	125,801,108 (GRCm39)	unclassified	probably benign
R2045:Lypd1	UTSW	1	125,838,272 (GRCm39)	splice site	probably benign
R3757:Lypd1	UTSW	1	125,838,121 (GRCm39)	splice site	probably benign
R7453:Lypd1	UTSW	1	125,801,303 (GRCm39)	missense	probably benign
R8916:Lypd1	UTSW	1	125,801,120 (GRCm39)	missense	unknown

Predicted Primers

PCR Primer
(F):5'- CCCAAGTGCATGTGTAACAC -3'
(R):5'- TCCAGCCTTCCTGAACATCAG -3'

Sequencing Primer
(F):5'- GTGTGTTACATCAGTCAGG -3'
(R):5'- CCAGAAGCCCTTGTTGTCTGG -3'

Posted On

2018-11-06