Mutagenetix > Incidental Mutation

Incidental Mutation 'R6014:Lrrc4c'

479897

Institutional Source

Beutler Lab

Gene Symbol

Lrrc4c

Ensembl Gene

ENSMUSG00000050587

Gene Name

leucine rich repeat containing 4C

Synonyms

6430556C10Rik, netrin g1 ligand, NGL-1

MMRRC Submission

044190-MU

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.099) question?

Stock #

R6014 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

96148514-97462011 bp(+) (GRCm39)

Type of Mutation

splice site (149 bp from exon)

DNA Base Change (assembly)

T to G at 97459557 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Ref Sequence

ENSEMBL: ENSMUSP00000128490 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000059049] [ENSMUST00000135431] [ENSMUST00000162807] [ENSMUST00000170144]

AlphaFold

Q8C031

Predicted Effect

possibly damaging
Transcript: ENSMUST00000059049
AA Change: I61S

PolyPhen 2 Score 0.495 (Sensitivity: 0.88; Specificity: 0.90)

SMART Domains

Protein: ENSMUSP00000131795
Gene: ENSMUSG00000050587
AA Change: I61S

Domain	Start	End	E-Value	Type
low complexity region	26	42	N/A	INTRINSIC
LRRNT	46	80	6.95e-4	SMART
LRR	79	98	1.97e2	SMART
LRR_TYP	99	122	7.37e-4	SMART
LRR	123	146	1.08e-1	SMART
LRR_TYP	147	170	1.38e-3	SMART
Blast:LRR	171	195	5e-8	BLAST
LRR	196	217	8.03e1	SMART
LRR_TYP	218	241	2.12e-4	SMART
LRR	242	265	6.97e1	SMART
LRR_TYP	266	289	2.53e-2	SMART
LRRCT	301	352	2.68e-2	SMART
IGc2	366	433	1.22e-7	SMART
transmembrane domain	526	548	N/A	INTRINSIC

Predicted Effect

possibly damaging
Transcript: ENSMUST00000135431
AA Change: I61S

PolyPhen 2 Score 0.495 (Sensitivity: 0.88; Specificity: 0.90)

SMART Domains

Protein: ENSMUSP00000130984
Gene: ENSMUSG00000050587
AA Change: I61S

Domain	Start	End	E-Value	Type
low complexity region	26	42	N/A	INTRINSIC
LRRNT	46	80	6.95e-4	SMART
LRR	79	98	1.97e2	SMART
LRR_TYP	99	122	7.37e-4	SMART
LRR	123	146	1.08e-1	SMART
LRR_TYP	147	170	1.38e-3	SMART
Blast:LRR	171	195	5e-8	BLAST
LRR	196	217	8.03e1	SMART
LRR_TYP	218	241	2.12e-4	SMART
LRR	242	265	6.97e1	SMART
LRR_TYP	266	289	2.53e-2	SMART
LRRCT	301	352	2.68e-2	SMART
IGc2	366	433	1.22e-7	SMART
transmembrane domain	526	548	N/A	INTRINSIC

Predicted Effect

possibly damaging
Transcript: ENSMUST00000162807
AA Change: I61S

PolyPhen 2 Score 0.495 (Sensitivity: 0.88; Specificity: 0.90)

SMART Domains

Protein: ENSMUSP00000125218
Gene: ENSMUSG00000050587
AA Change: I61S

Domain	Start	End	E-Value	Type
low complexity region	26	42	N/A	INTRINSIC
LRRNT	46	80	6.95e-4	SMART
LRR	79	98	1.97e2	SMART
LRR_TYP	99	122	7.37e-4	SMART
LRR	123	146	1.08e-1	SMART
LRR_TYP	147	170	1.38e-3	SMART
Blast:LRR	171	195	5e-8	BLAST
LRR	196	217	8.03e1	SMART
LRR_TYP	218	241	2.12e-4	SMART
LRR	242	265	6.97e1	SMART
LRR_TYP	266	289	2.53e-2	SMART
LRRCT	301	352	2.68e-2	SMART
IGc2	366	433	1.22e-7	SMART
transmembrane domain	526	548	N/A	INTRINSIC

Predicted Effect

probably null
Transcript: ENSMUST00000170144

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000199276

Meta Mutation Damage Score

0.0859

Coding Region Coverage

1x: 99.9%
3x: 99.5%
10x: 97.8%
20x: 93.3%

Validation Efficiency

100% (67/67)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] NGL1 is a specific binding partner for netrin G1 (NTNG1; MIM 608818), which is a member of the netrin family of axon guidance molecules (Lin et al., 2003 [PubMed 14595443]).[supplied by OMIM, Mar 2008]
PHENOTYPE: Homozygous mutant mice exhibited an increased mean serum IL-6 response to LPS challenge when compared with controls. No other notable phenotype was detected in a high-througput screen. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 67 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4930568D16Rik	A	T	2: 35,244,881 (GRCm39)	M157K	probably benign	Het
A2ml1	C	T	6: 128,548,948 (GRCm39)	C278Y	probably damaging	Het
Abcc2	A	T	19: 43,815,174 (GRCm39)	Q1187L	probably benign	Het
Adcy9	A	T	16: 4,236,683 (GRCm39)	Y6N	probably damaging	Het
Adh1	T	C	3: 137,992,559 (GRCm39)	I225T	probably benign	Het
Akap11	A	T	14: 78,749,939 (GRCm39)	I816K	probably benign	Het
Ap1b1	T	A	11: 4,969,364 (GRCm39)	M240K	possibly damaging	Het
Apex1	A	T	14: 51,162,982 (GRCm39)	T17S	probably benign	Het
Arhgap21	C	T	2: 20,886,616 (GRCm39)	G26D	probably damaging	Het
Bahcc1	A	G	11: 120,180,615 (GRCm39)	Y2613C	probably benign	Het
Baz1b	C	T	5: 135,246,248 (GRCm39)	R566W	probably damaging	Het
Casp8ap2	A	T	4: 32,641,400 (GRCm39)	Y818F	probably damaging	Het
Col3a1	T	A	1: 45,360,739 (GRCm39)	C56*	probably null	Het
Coro2a	G	A	4: 46,542,261 (GRCm39)	P371S	probably damaging	Het
Cyp2a22	T	A	7: 26,638,605 (GRCm39)		probably null	Het
Dpysl3	T	A	18: 43,494,132 (GRCm39)	I183F	probably damaging	Het
Drc1	A	T	5: 30,502,993 (GRCm39)	N172I	probably damaging	Het
Dst	T	C	1: 34,303,915 (GRCm39)	Y1378H	probably damaging	Het
Dync2i2	C	T	2: 29,921,763 (GRCm39)	A533T	probably benign	Het
Eml2	G	A	7: 18,935,088 (GRCm39)	V432I	probably damaging	Het
Epb41l3	A	T	17: 69,590,955 (GRCm39)	T91S	probably damaging	Het
Exoc4	T	C	6: 33,452,932 (GRCm39)	V474A	probably benign	Het
Fam229b	G	A	10: 38,994,989 (GRCm39)	T56I	probably damaging	Het
Gfm2	A	G	13: 97,288,169 (GRCm39)		probably null	Het
Git2	C	T	5: 114,871,938 (GRCm39)	E152K	probably benign	Het
Golt1b	T	A	6: 142,341,943 (GRCm39)	I109N	probably damaging	Het
Grid2ip	T	A	5: 143,373,578 (GRCm39)	M783K	possibly damaging	Het
Inpp5a	A	G	7: 139,154,898 (GRCm39)	Y339C	probably damaging	Het
Isoc2a	T	C	7: 4,894,625 (GRCm39)	S103P	probably damaging	Het
Itih4	C	A	14: 30,614,586 (GRCm39)	Q483K	probably benign	Het
Kansl2	A	G	15: 98,418,197 (GRCm39)		probably null	Het
Kdm5d	G	A	Y: 921,528 (GRCm39)	A509T	probably benign	Het
Krt13	A	T	11: 100,008,437 (GRCm39)	D433E	unknown	Het
Lat2	C	T	5: 134,632,308 (GRCm39)	V142M	probably damaging	Het
Lemd1	A	C	1: 132,184,463 (GRCm39)	*102S	probably null	Het
Lrfn2	T	C	17: 49,376,934 (GRCm39)	L5P	possibly damaging	Het
Lypla1	T	A	1: 4,878,594 (GRCm39)		probably null	Het
Magi2	G	A	5: 20,816,091 (GRCm39)	G744R	probably damaging	Het
Myh14	T	A	7: 44,274,502 (GRCm39)	E948V	probably null	Het
Myo5a	C	A	9: 75,074,489 (GRCm39)	Y799*	probably null	Het
Nacc1	A	C	8: 85,401,700 (GRCm39)	M371R	possibly damaging	Het
Nlrp5	T	G	7: 23,109,372 (GRCm39)	M106R	probably benign	Het
Oas1h	C	T	5: 121,005,229 (GRCm39)	H226Y	possibly damaging	Het
Obscn	A	C	11: 58,929,690 (GRCm39)	I5175R	probably damaging	Het
Pcdh7	T	A	5: 57,878,497 (GRCm39)	I684N	probably damaging	Het
Pcdhb3	T	A	18: 37,435,706 (GRCm39)	N557K	probably damaging	Het
Pde3b	T	C	7: 114,015,675 (GRCm39)	L297S	probably damaging	Het
Pigv	G	T	4: 133,392,740 (GRCm39)	H143Q	probably benign	Het
Ptk2	T	G	15: 73,176,293 (GRCm39)	Y251S	possibly damaging	Het
Ralgds	A	G	2: 28,433,673 (GRCm39)	N219S	probably damaging	Het
Sardh	C	A	2: 27,087,540 (GRCm39)		probably null	Het
Serpina3b	A	T	12: 104,097,356 (GRCm39)	K212N	possibly damaging	Het
Sh3bp2	A	G	5: 34,716,971 (GRCm39)	N461D	probably benign	Het
Shisa2	A	T	14: 59,867,357 (GRCm39)	Q203L	probably damaging	Het
Shmt1	C	A	11: 60,688,383 (GRCm39)	G255V	probably damaging	Het
Socs1	T	A	16: 10,602,357 (GRCm39)	I127F	possibly damaging	Het
Srcap	A	T	7: 127,137,922 (GRCm39)	T1091S	probably benign	Het
Syt14	A	G	1: 192,613,003 (GRCm39)	I599T	probably damaging	Het
Tep1	A	T	14: 51,084,457 (GRCm39)	N907K	probably benign	Het
Themis2	A	G	4: 132,513,291 (GRCm39)	Y312H	probably benign	Het
Tubgcp5	T	G	7: 55,473,357 (GRCm39)	S812A	probably benign	Het
Ush2a	A	T	1: 188,582,237 (GRCm39)	I3767F	probably damaging	Het
Usp40	T	A	1: 87,907,738 (GRCm39)	E626V	probably damaging	Het
Utrn	T	C	10: 12,566,620 (GRCm39)	R1181G	probably benign	Het
Vmn2r117	T	A	17: 23,698,535 (GRCm39)	I13F	probably damaging	Het
Wdr48	G	T	9: 119,753,775 (GRCm39)	V646F	probably damaging	Het
Wdr64	T	C	1: 175,633,556 (GRCm39)	F936L	possibly damaging	Het

Other mutations in Lrrc4c

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00482:Lrrc4c	APN	2	97,460,730 (GRCm39)	nonsense	probably null
IGL02095:Lrrc4c	APN	2	97,459,749 (GRCm39)	missense	probably benign	0.05
IGL02165:Lrrc4c	APN	2	97,459,378 (GRCm39)	start codon destroyed	probably null	0.33
IGL02176:Lrrc4c	APN	2	97,460,598 (GRCm39)	missense	probably damaging	0.96
IGL02674:Lrrc4c	APN	2	97,460,120 (GRCm39)	missense	probably damaging	0.99
IGL03082:Lrrc4c	APN	2	97,460,931 (GRCm39)	missense	probably benign	0.05
IGL03303:Lrrc4c	APN	2	97,459,937 (GRCm39)	missense	probably damaging	1.00
R0946:Lrrc4c	UTSW	2	97,459,809 (GRCm39)	missense	probably benign	0.00
R1037:Lrrc4c	UTSW	2	97,460,330 (GRCm39)	missense	probably benign
R1518:Lrrc4c	UTSW	2	97,460,921 (GRCm39)	missense	probably benign
R1559:Lrrc4c	UTSW	2	97,461,117 (GRCm39)	missense	probably benign	0.00
R2192:Lrrc4c	UTSW	2	97,459,657 (GRCm39)	missense	possibly damaging	0.50
R2213:Lrrc4c	UTSW	2	97,460,816 (GRCm39)	missense	probably benign	0.29
R2279:Lrrc4c	UTSW	2	97,460,850 (GRCm39)	missense	possibly damaging	0.86
R3552:Lrrc4c	UTSW	2	97,460,306 (GRCm39)	missense	probably damaging	1.00
R3840:Lrrc4c	UTSW	2	97,460,537 (GRCm39)	missense	probably damaging	0.98
R3841:Lrrc4c	UTSW	2	97,460,537 (GRCm39)	missense	probably damaging	0.98
R4606:Lrrc4c	UTSW	2	97,460,658 (GRCm39)	missense	probably benign	0.22
R4938:Lrrc4c	UTSW	2	97,459,646 (GRCm39)	missense	probably damaging	1.00
R4946:Lrrc4c	UTSW	2	97,460,834 (GRCm39)	missense	probably benign	0.00
R5323:Lrrc4c	UTSW	2	97,460,498 (GRCm39)	missense	probably damaging	1.00
R6297:Lrrc4c	UTSW	2	97,459,964 (GRCm39)	missense	probably damaging	0.99
R6376:Lrrc4c	UTSW	2	97,459,391 (GRCm39)	missense	probably benign	0.03
R7032:Lrrc4c	UTSW	2	97,459,410 (GRCm39)	missense	probably benign
R7419:Lrrc4c	UTSW	2	97,460,106 (GRCm39)	missense	probably benign	0.07
R7699:Lrrc4c	UTSW	2	97,461,024 (GRCm39)	missense	possibly damaging	0.81
R7700:Lrrc4c	UTSW	2	97,461,024 (GRCm39)	missense	possibly damaging	0.81
R7723:Lrrc4c	UTSW	2	97,460,999 (GRCm39)	missense	possibly damaging	0.91
R7736:Lrrc4c	UTSW	2	97,460,705 (GRCm39)	missense	probably benign	0.02
R7843:Lrrc4c	UTSW	2	97,460,558 (GRCm39)	missense	probably benign	0.19
R7880:Lrrc4c	UTSW	2	97,461,143 (GRCm39)	missense	probably benign	0.08
R8008:Lrrc4c	UTSW	2	97,460,594 (GRCm39)	missense	possibly damaging	0.88
R8479:Lrrc4c	UTSW	2	97,459,977 (GRCm39)	missense	probably damaging	1.00
R8802:Lrrc4c	UTSW	2	97,460,603 (GRCm39)	missense	possibly damaging	0.83
R8821:Lrrc4c	UTSW	2	97,460,040 (GRCm39)	missense	possibly damaging	0.88
R8906:Lrrc4c	UTSW	2	97,460,393 (GRCm39)	missense	probably benign	0.00
R8933:Lrrc4c	UTSW	2	97,459,826 (GRCm39)	missense	probably benign	0.36
R8974:Lrrc4c	UTSW	2	97,459,992 (GRCm39)	missense	probably damaging	1.00
R9115:Lrrc4c	UTSW	2	97,459,686 (GRCm39)	missense	probably benign	0.00
R9266:Lrrc4c	UTSW	2	97,459,853 (GRCm39)	missense	probably benign	0.26
R9311:Lrrc4c	UTSW	2	97,461,080 (GRCm39)	missense	possibly damaging	0.90
Z1177:Lrrc4c	UTSW	2	97,460,828 (GRCm39)	nonsense	probably null

Predicted Primers

PCR Primer
(F):5'- TGTTTGAACTCCAGAAGGACCAAC -3'
(R):5'- TGAAGGCCCCGATTTCAATGG -3'

Sequencing Primer
(F):5'- ATGTTGAACAAGATGACCTTACATCC -3'
(R):5'- CCCCGATTTCAATGGTTCGAATATGG -3'

Posted On

2017-06-26