Mutagenetix > Incidental Mutation

Incidental Mutation 'R1852:Chl1'

226068

Institutional Source

Beutler Lab

Gene Symbol

Chl1

Ensembl Gene

ENSMUSG00000030077

Gene Name

cell adhesion molecule L1-like

Synonyms

A530023M13Rik, close homolog of L1, LICAM2, CALL

MMRRC Submission

039876-MU

Accession Numbers

Essential gene?

Possibly essential (E-score: 0.524) question?

Stock #

R1852 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

103487372-103709999 bp(+) (GRCm39)

Type of Mutation

splice site

DNA Base Change (assembly)

A to T at 103676120 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Ref Sequence

ENSEMBL: ENSMUSP00000144739 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000066905] [ENSMUST00000203830] [ENSMUST00000203912] [ENSMUST00000205098]

AlphaFold

P70232

Predicted Effect

probably null
Transcript: ENSMUST00000066905

SMART Domains

Protein: ENSMUSP00000063933
Gene: ENSMUSG00000030077

Domain	Start	End	E-Value	Type
signal peptide	1	25	N/A	INTRINSIC
IG_like	48	116	3.14e-2	SMART
IG	138	225	1.36e-5	SMART
IGc2	253	317	3.76e-17	SMART
IGc2	343	408	1.61e-7	SMART
IGc2	436	501	1.56e-5	SMART
IG	521	609	6.02e-7	SMART
IG_like	539	598	1.27e-1	SMART
FN3	612	695	2.24e-13	SMART
FN3	712	794	1.92e-3	SMART
FN3	810	901	2.3e-1	SMART
FN3	916	1002	4.09e-7	SMART
transmembrane domain	1082	1104	N/A	INTRINSIC
Pfam:Bravo_FIGEY	1105	1190	3.9e-33	PFAM

Predicted Effect

probably null
Transcript: ENSMUST00000203830

SMART Domains

Protein: ENSMUSP00000144758
Gene: ENSMUSG00000030077

Domain	Start	End	E-Value	Type
signal peptide	1	25	N/A	INTRINSIC
IG_like	48	116	3.14e-2	SMART
IG	138	225	1.36e-5	SMART
IGc2	253	317	3.76e-17	SMART
IGc2	343	408	1.61e-7	SMART
IGc2	436	501	1.56e-5	SMART
IG	521	609	6.02e-7	SMART
IG_like	539	598	1.27e-1	SMART
FN3	612	695	2.24e-13	SMART
FN3	712	794	1.92e-3	SMART
FN3	810	901	2.3e-1	SMART
FN3	916	1002	4.09e-7	SMART
transmembrane domain	1082	1104	N/A	INTRINSIC
Pfam:Bravo_FIGEY	1105	1190	3.9e-33	PFAM

Predicted Effect

probably null
Transcript: ENSMUST00000203912

SMART Domains

Protein: ENSMUSP00000145026
Gene: ENSMUSG00000030077

Domain	Start	End	E-Value	Type
signal peptide	1	25	N/A	INTRINSIC
IG_like	48	116	3.14e-2	SMART
IG	138	225	1.36e-5	SMART
IGc2	269	333	3.76e-17	SMART
IGc2	359	424	1.61e-7	SMART
IGc2	452	517	1.56e-5	SMART
IG	537	625	6.02e-7	SMART
IG_like	555	614	1.27e-1	SMART
FN3	628	711	2.24e-13	SMART
FN3	728	810	1.92e-3	SMART
FN3	826	917	2.3e-1	SMART
FN3	932	1018	4.09e-7	SMART
transmembrane domain	1044	1066	N/A	INTRINSIC
Pfam:Bravo_FIGEY	1067	1131	2.5e-12	PFAM

Predicted Effect

probably null
Transcript: ENSMUST00000205098

SMART Domains

Protein: ENSMUSP00000144739
Gene: ENSMUSG00000030077

Domain	Start	End	E-Value	Type
FN3	4	67	4.4e-1	SMART
FN3	83	174	1.2e-3	SMART
FN3	189	275	2.1e-9	SMART
transmembrane domain	301	323	N/A	INTRINSIC
Pfam:Bravo_FIGEY	324	409	3.6e-30	PFAM

Coding Region Coverage

1x: 97.4%
3x: 96.8%
10x: 95.0%
20x: 91.6%

Validation Efficiency

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The protein encoded by this gene is a member of the L1 gene family of neural cell adhesion molecules. It is a neural recognition molecule that may be involved in signal transduction pathways. The deletion of one copy of this gene may be responsible for mental defects in patients with 3p- syndrome. This protein may also play a role in the growth of certain cancers. Alternate splicing results in both coding and non-coding variants. [provided by RefSeq, Nov 2011]
PHENOTYPE: Homozygous mutation of this gene results in enlargement of the lateral ventricles and altered hippocampal mossy fiber organization. Mutant animals exhibit altered exploratory behavior. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 106 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
2900092C05Rik	A	G	7: 12,246,629 (GRCm39)		probably null	Het
4930433I11Rik	T	A	7: 40,643,037 (GRCm39)	D326E	probably benign	Het
Abca8a	T	C	11: 109,960,212 (GRCm39)	D676G	probably damaging	Het
Abcb7	T	C	X: 103,349,005 (GRCm39)	M153V	probably benign	Het
Ablim3	G	A	18: 61,982,466 (GRCm39)	H160Y	probably benign	Het
Acsl6	T	C	11: 54,251,902 (GRCm39)	I683T	probably damaging	Het
Adgrg5	A	T	8: 95,664,428 (GRCm39)	Y345F	probably damaging	Het
Alg6	T	G	4: 99,634,599 (GRCm39)	F114V	probably benign	Het
Ank2	A	C	3: 126,791,500 (GRCm39)		probably null	Het
Ankrd24	A	T	10: 81,478,775 (GRCm39)		probably benign	Het
Ano8	T	C	8: 71,936,131 (GRCm39)	K222E	probably damaging	Het
Arhgef5	T	C	6: 43,252,119 (GRCm39)	S957P	probably benign	Het
Bltp2	A	G	11: 78,159,299 (GRCm39)	D499G	probably damaging	Het
Bmpr1b	A	T	3: 141,563,163 (GRCm39)		probably null	Het
C3	A	G	17: 57,529,823 (GRCm39)	V2A	probably damaging	Het
Capn1	A	G	19: 6,059,133 (GRCm39)	V276A	possibly damaging	Het
Ccdc57	T	C	11: 120,812,499 (GRCm39)	E85G	probably damaging	Het
Chil3	C	T	3: 106,056,117 (GRCm39)		probably null	Het
Chodl	C	T	16: 78,738,146 (GRCm39)	P38L	probably benign	Het
Clec4a2	G	T	6: 123,116,084 (GRCm39)	E124*	probably null	Het
Cmtr1	T	C	17: 29,921,229 (GRCm39)	V825A	probably benign	Het
Cnksr3	T	C	10: 7,070,539 (GRCm39)	I232V	probably benign	Het
Cntn1	C	T	15: 92,203,021 (GRCm39)	R768C	probably damaging	Het
Col15a1	G	T	4: 47,299,278 (GRCm39)		probably null	Het
Col6a3	T	A	1: 90,735,256 (GRCm39)	I798F	possibly damaging	Het
Cpxcr1	T	A	X: 115,387,758 (GRCm39)	L223*	probably null	Het
Cul1	A	G	6: 47,497,764 (GRCm39)	N615S	probably damaging	Het
Cxcr2	A	G	1: 74,198,438 (GRCm39)	I311V	probably benign	Het
Cyp2c67	C	T	19: 39,605,811 (GRCm39)	G362S	probably benign	Het
D930048N14Rik	T	A	11: 51,544,692 (GRCm39)		probably benign	Het
Ddx49	T	C	8: 70,753,633 (GRCm39)	T79A	probably damaging	Het
Defb46	T	A	8: 19,289,991 (GRCm39)		probably null	Het
Dnah17	T	A	11: 118,012,742 (GRCm39)	I145F	probably damaging	Het
Dock8	A	T	19: 25,104,492 (GRCm39)	I725F	probably benign	Het
Dppa4	G	A	16: 48,108,247 (GRCm39)	A11T	probably damaging	Het
Enam	T	A	5: 88,652,324 (GRCm39)	S1278T	possibly damaging	Het
Fndc3a	A	G	14: 72,794,283 (GRCm39)	V829A	probably damaging	Het
Gatb	T	G	3: 85,526,184 (GRCm39)	L354R	probably damaging	Het
Gm10787	A	T	10: 76,857,711 (GRCm39)		noncoding transcript	Het
Gsap	T	A	5: 21,495,543 (GRCm39)		probably null	Het
Gtf2ird1	T	C	5: 134,411,434 (GRCm39)		probably null	Het
Has3	A	T	8: 107,600,711 (GRCm39)	I58F	probably damaging	Het
Haus5	A	T	7: 30,357,926 (GRCm39)		probably null	Het
Hip1r	T	C	5: 124,129,568 (GRCm39)	V169A	probably benign	Het
Hnf1a	T	A	5: 115,108,770 (GRCm39)	D45V	probably damaging	Het
Il20ra	T	A	10: 19,618,767 (GRCm39)	Y72N	probably damaging	Het
Ipo11	A	T	13: 106,948,765 (GRCm39)	V914E	possibly damaging	Het
Itpr1	T	C	6: 108,363,667 (GRCm39)	L763P	probably damaging	Het
Katnal2	C	A	18: 77,103,719 (GRCm39)	R104L	probably benign	Het
Kcng4	G	T	8: 120,352,947 (GRCm39)	P321Q	probably benign	Het
Larp4b	T	C	13: 9,187,339 (GRCm39)		probably null	Het
Lars1	T	C	18: 42,345,673 (GRCm39)	N1001S	probably benign	Het
Lhcgr	T	A	17: 89,072,604 (GRCm39)	I148F	probably damaging	Het
Lsm10	T	A	4: 125,991,756 (GRCm39)	S37R	possibly damaging	Het
Mfsd13a	A	G	19: 46,360,619 (GRCm39)		probably null	Het
Mipep	T	A	14: 61,080,689 (GRCm39)	C560*	probably null	Het
Mme	G	A	3: 63,235,467 (GRCm39)	D172N	probably benign	Het
Mme	A	G	3: 63,235,404 (GRCm39)	S97G	probably benign	Het
Mtrex	A	T	13: 113,009,461 (GRCm39)	H979Q	probably benign	Het
Mx1	A	T	16: 97,249,403 (GRCm39)	L608Q	probably damaging	Het
Myt1l	T	C	12: 29,901,660 (GRCm39)	M208T	probably benign	Het
Neb	T	C	2: 52,118,554 (GRCm39)	I3987V	probably damaging	Het
Nelfcd	A	G	2: 174,265,771 (GRCm39)		probably null	Het
Neto1	T	C	18: 86,414,009 (GRCm39)	M1T	probably null	Het
Nom1	T	C	5: 29,651,876 (GRCm39)	F738S	possibly damaging	Het
Or10v1	C	A	19: 11,874,249 (GRCm39)	P288H	probably damaging	Het
Or4f61	C	A	2: 111,922,192 (GRCm39)	V285L	probably benign	Het
Or51h5	C	T	7: 102,577,648 (GRCm39)	S271L	probably damaging	Het
Or5b123	C	T	19: 13,596,967 (GRCm39)	S147F	probably damaging	Het
Or5w14	T	C	2: 87,541,317 (GRCm39)		probably null	Het
Or6c203	T	C	10: 129,010,197 (GRCm39)	K231R	probably benign	Het
Or6f2	T	A	7: 139,756,474 (GRCm39)	L147*	probably null	Het
Or9m1b	T	G	2: 87,836,865 (GRCm39)	I86L	probably damaging	Het
Pak1ip1	A	G	13: 41,164,708 (GRCm39)	T264A	possibly damaging	Het
Palb2	G	T	7: 121,713,537 (GRCm39)	D915E	possibly damaging	Het
Pank4	T	C	4: 155,060,816 (GRCm39)	L491P	probably damaging	Het
Paqr7	T	C	4: 134,234,980 (GRCm39)	V279A	probably benign	Het
Pcif1	G	A	2: 164,730,386 (GRCm39)	R373Q	probably damaging	Het
Pdgfa	T	A	5: 138,964,927 (GRCm39)	N185I	probably benign	Het
Plcd4	T	C	1: 74,588,520 (GRCm39)	V123A	possibly damaging	Het
Pramel26	T	C	4: 143,539,396 (GRCm39)	I32M	probably benign	Het
Prune2	A	G	19: 17,176,503 (GRCm39)	I154V	probably damaging	Het
Rac3	T	G	11: 120,614,320 (GRCm39)	L148R	possibly damaging	Het
Rapgef6	T	A	11: 54,533,637 (GRCm39)	D362E	probably benign	Het
Rbl1	A	G	2: 157,016,823 (GRCm39)	I592T	probably benign	Het
Rbl2	A	C	8: 91,822,191 (GRCm39)	D408A	possibly damaging	Het
Retreg2	A	G	1: 75,123,319 (GRCm39)	K416E	probably benign	Het
Rorb	A	T	19: 18,939,447 (GRCm39)	L234H	probably damaging	Het
Rpp40	T	G	13: 36,080,897 (GRCm39)	D279A	probably benign	Het
Siglec1	C	A	2: 130,923,420 (GRCm39)	V442L	probably damaging	Het
Sik3	C	G	9: 46,132,387 (GRCm39)	H1276Q	probably benign	Het
Slc25a34	G	A	4: 141,349,579 (GRCm39)	T192I	probably benign	Het
Sp140l1	G	A	1: 85,062,852 (GRCm39)		probably benign	Het
Sptbn5	T	C	2: 119,902,125 (GRCm39)	I126M	possibly damaging	Het
Strada	A	G	11: 106,062,047 (GRCm39)	V94A	possibly damaging	Het
Stxbp5	C	A	10: 9,688,042 (GRCm39)	V420F	possibly damaging	Het
Tgm1	T	C	14: 55,942,398 (GRCm39)	Y651C	probably damaging	Het
Tmem200c	T	A	17: 69,147,612 (GRCm39)	V65E	probably damaging	Het
Tmem74	A	T	15: 43,730,559 (GRCm39)	D161E	probably benign	Het
Trgc3	A	T	13: 19,445,261 (GRCm39)	M70L	probably damaging	Het
Vcan	T	G	13: 89,853,511 (GRCm39)	E483A	probably damaging	Het
Vmn2r124	A	G	17: 18,283,436 (GRCm39)	T377A	probably benign	Het
Vmn2r3	A	C	3: 64,166,815 (GRCm39)	I772S	probably damaging	Het
Wdfy3	A	G	5: 102,063,242 (GRCm39)	V1342A	probably benign	Het
Zfp507	T	C	7: 35,487,176 (GRCm39)	H764R	probably damaging	Het
Znrf3	A	G	11: 5,237,455 (GRCm39)	I218T	possibly damaging	Het

Other mutations in Chl1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00590:Chl1	APN	6	103,670,022 (GRCm39)	missense	probably benign	0.08
IGL00786:Chl1	APN	6	103,652,106 (GRCm39)	missense	probably damaging	1.00
IGL00959:Chl1	APN	6	103,686,211 (GRCm39)	splice site	probably null
IGL01109:Chl1	APN	6	103,692,354 (GRCm39)	missense	probably damaging	1.00
IGL01354:Chl1	APN	6	103,642,814 (GRCm39)	missense	probably benign	0.01
IGL01367:Chl1	APN	6	103,706,186 (GRCm39)	missense	probably benign	0.42
IGL01371:Chl1	APN	6	103,692,325 (GRCm39)	missense	probably damaging	1.00
IGL01599:Chl1	APN	6	103,685,445 (GRCm39)	missense	probably benign	0.34
IGL01724:Chl1	APN	6	103,626,534 (GRCm39)	missense	probably damaging	1.00
IGL02001:Chl1	APN	6	103,619,017 (GRCm39)	missense	possibly damaging	0.90
IGL02066:Chl1	APN	6	103,675,185 (GRCm39)	missense	probably benign	0.39
IGL02122:Chl1	APN	6	103,652,098 (GRCm39)	missense	probably benign	0.39
IGL02340:Chl1	APN	6	103,675,086 (GRCm39)	missense	probably damaging	1.00
IGL02420:Chl1	APN	6	103,692,330 (GRCm39)	missense	probably damaging	1.00
IGL02421:Chl1	APN	6	103,694,541 (GRCm39)	missense	probably damaging	1.00
IGL02429:Chl1	APN	6	103,641,770 (GRCm39)	unclassified	probably benign
IGL02825:Chl1	APN	6	103,645,764 (GRCm39)	missense	possibly damaging	0.87
IGL02858:Chl1	APN	6	103,618,949 (GRCm39)	missense	probably damaging	1.00
IGL03169:Chl1	APN	6	103,642,928 (GRCm39)	missense	probably damaging	1.00
IGL03185:Chl1	APN	6	103,642,824 (GRCm39)	missense	probably damaging	1.00
IGL03189:Chl1	APN	6	103,660,168 (GRCm39)	missense	possibly damaging	0.91
IGL03288:Chl1	APN	6	103,652,058 (GRCm39)	missense	probably damaging	1.00
IGL03404:Chl1	APN	6	103,670,052 (GRCm39)	missense	probably damaging	1.00
IGL03052:Chl1	UTSW	6	103,668,628 (GRCm39)	missense	probably benign	0.01
R0060:Chl1	UTSW	6	103,688,019 (GRCm39)	splice site	probably benign
R0060:Chl1	UTSW	6	103,688,019 (GRCm39)	splice site	probably benign
R0062:Chl1	UTSW	6	103,726,613 (GRCm39)	missense	unknown
R0314:Chl1	UTSW	6	103,624,262 (GRCm39)	missense	probably damaging	1.00
R0322:Chl1	UTSW	6	103,678,844 (GRCm39)	splice site	probably benign
R0685:Chl1	UTSW	6	103,685,503 (GRCm39)	splice site	probably null
R0702:Chl1	UTSW	6	103,683,583 (GRCm39)	missense	probably damaging	1.00
R1056:Chl1	UTSW	6	103,652,038 (GRCm39)	missense	possibly damaging	0.66
R1138:Chl1	UTSW	6	103,670,140 (GRCm39)	missense	probably benign	0.05
R1483:Chl1	UTSW	6	103,624,248 (GRCm39)	missense	probably damaging	1.00
R1571:Chl1	UTSW	6	103,685,445 (GRCm39)	missense	probably benign	0.34
R1620:Chl1	UTSW	6	103,667,203 (GRCm39)	missense	probably benign	0.00
R1645:Chl1	UTSW	6	103,660,141 (GRCm39)	missense	probably benign	0.06
R1773:Chl1	UTSW	6	103,624,292 (GRCm39)	critical splice donor site	probably null
R1891:Chl1	UTSW	6	103,691,544 (GRCm39)	missense	possibly damaging	0.88
R2146:Chl1	UTSW	6	103,692,362 (GRCm39)	critical splice donor site	probably null
R2147:Chl1	UTSW	6	103,692,362 (GRCm39)	critical splice donor site	probably null
R2148:Chl1	UTSW	6	103,692,362 (GRCm39)	critical splice donor site	probably null
R2163:Chl1	UTSW	6	103,688,192 (GRCm39)	missense	probably damaging	1.00
R2291:Chl1	UTSW	6	103,692,354 (GRCm39)	missense	probably damaging	1.00
R2920:Chl1	UTSW	6	103,672,304 (GRCm39)	missense	probably damaging	1.00
R3611:Chl1	UTSW	6	103,675,116 (GRCm39)	missense	probably damaging	1.00
R3979:Chl1	UTSW	6	103,692,245 (GRCm39)	nonsense	probably null
R4987:Chl1	UTSW	6	103,651,938 (GRCm39)	missense	probably damaging	1.00
R5266:Chl1	UTSW	6	103,677,504 (GRCm39)	missense	probably damaging	1.00
R5478:Chl1	UTSW	6	103,660,182 (GRCm39)	missense	probably damaging	1.00
R5523:Chl1	UTSW	6	103,685,675 (GRCm39)	missense	probably damaging	1.00
R5887:Chl1	UTSW	6	103,694,565 (GRCm39)	missense	probably benign	0.00
R5986:Chl1	UTSW	6	103,686,152 (GRCm39)	missense	probably benign	0.45
R6101:Chl1	UTSW	6	103,669,993 (GRCm39)	missense	probably damaging	0.96
R6179:Chl1	UTSW	6	103,660,204 (GRCm39)	missense	probably benign	0.38
R6366:Chl1	UTSW	6	103,706,197 (GRCm39)	missense	possibly damaging	0.95
R6634:Chl1	UTSW	6	103,667,220 (GRCm39)	missense	probably damaging	1.00
R6824:Chl1	UTSW	6	103,691,510 (GRCm39)	missense	probably damaging	1.00
R6913:Chl1	UTSW	6	103,642,909 (GRCm39)	nonsense	probably null
R7097:Chl1	UTSW	6	103,683,409 (GRCm39)	missense	probably damaging	1.00
R7122:Chl1	UTSW	6	103,683,409 (GRCm39)	missense	probably damaging	1.00
R7198:Chl1	UTSW	6	103,683,517 (GRCm39)	missense	probably damaging	1.00
R7203:Chl1	UTSW	6	103,668,635 (GRCm39)	missense	probably benign	0.13
R7527:Chl1	UTSW	6	103,688,162 (GRCm39)	missense	probably damaging	1.00
R7625:Chl1	UTSW	6	103,706,086 (GRCm39)	missense	probably damaging	1.00
R7667:Chl1	UTSW	6	103,672,456 (GRCm39)	missense	possibly damaging	0.82
R7683:Chl1	UTSW	6	103,668,613 (GRCm39)	missense	possibly damaging	0.72
R7712:Chl1	UTSW	6	103,688,063 (GRCm39)	missense	possibly damaging	0.94
R7838:Chl1	UTSW	6	103,668,635 (GRCm39)	missense	probably benign	0.01
R7863:Chl1	UTSW	6	103,683,475 (GRCm39)	missense	possibly damaging	0.46
R7874:Chl1	UTSW	6	103,667,224 (GRCm39)	missense	probably benign	0.22
R7998:Chl1	UTSW	6	103,706,250 (GRCm39)	missense	probably benign	0.01
R8044:Chl1	UTSW	6	103,683,593 (GRCm39)	missense	probably damaging	0.96
R8059:Chl1	UTSW	6	103,651,948 (GRCm39)	missense	probably damaging	0.97
R8462:Chl1	UTSW	6	103,706,130 (GRCm39)	missense	probably benign	0.11
R8558:Chl1	UTSW	6	103,685,390 (GRCm39)	missense	probably benign	0.14
R8827:Chl1	UTSW	6	103,670,111 (GRCm39)	missense	probably benign
R8865:Chl1	UTSW	6	103,685,822 (GRCm39)	missense	probably damaging	0.99
R8939:Chl1	UTSW	6	103,642,868 (GRCm39)	missense	probably damaging	1.00
R9092:Chl1	UTSW	6	103,645,815 (GRCm39)	unclassified	probably benign
Z1177:Chl1	UTSW	6	103,674,910 (GRCm39)	start gained	probably benign
Z1177:Chl1	UTSW	6	103,670,057 (GRCm39)	nonsense	probably null
Z1191:Chl1	UTSW	6	103,660,172 (GRCm39)	missense	probably damaging	1.00

Predicted Primers

Posted On

2014-09-11