Mutagenetix > Incidental Mutation

Incidental Mutation 'IGL01599:Chl1'

92031

Institutional Source

Australian Phenomics Network (link to record)

Gene Symbol

Chl1

Ensembl Gene

ENSMUSG00000030077

Gene Name

cell adhesion molecule L1-like

Synonyms

A530023M13Rik, LICAM2, close homolog of L1, CALL

Accession Numbers

Essential gene?

Possibly non essential (E-score: 0.411) question?

Stock #

IGL01599

Quality Score

Status

Chromosome

Chromosomal Location

103510586-103750211 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 103708484 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Threonine to Alanine at position 829 (T829A)

Ref Sequence

ENSEMBL: ENSMUSP00000144758 (fasta)

Gene Model

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

AlphaFold

P70232

Predicted Effect

probably benign
Transcript: ENSMUST00000066905
AA Change: T829A

PolyPhen 2 Score 0.337 (Sensitivity: 0.90; Specificity: 0.89)

SMART Domains

Protein: ENSMUSP00000063933
Gene: ENSMUSG00000030077
AA Change: T829A

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 benign
Transcript: ENSMUST00000203830
AA Change: T829A

PolyPhen 2 Score 0.337 (Sensitivity: 0.90; Specificity: 0.89)

SMART Domains

Protein: ENSMUSP00000144758
Gene: ENSMUSG00000030077
AA Change: T829A

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 benign
Transcript: ENSMUST00000203912
AA Change: T845A

PolyPhen 2 Score 0.210 (Sensitivity: 0.92; Specificity: 0.88)

SMART Domains

Protein: ENSMUSP00000145026
Gene: ENSMUSG00000030077
AA Change: T845A

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 benign
Transcript: ENSMUST00000205098
AA Change: T102A

PolyPhen 2 Score 0.013 (Sensitivity: 0.96; Specificity: 0.78)

SMART Domains

Protein: ENSMUSP00000144739
Gene: ENSMUSG00000030077
AA Change: T102A

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

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: 61 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Ackr3	T	C	1: 90,214,134	V105A	probably benign	Het
Acr	T	C	15: 89,568,414	V18A	probably benign	Het
Adgra2	G	A	8: 27,118,733	A540T	possibly damaging	Het
Aldh16a1	A	G	7: 45,142,093	F753L	probably damaging	Het
Ankfy1	T	A	11: 72,738,365	Y338N	probably benign	Het
Aox3	C	T	1: 58,169,794	R829C	probably damaging	Het
Arhgef11	T	C	3: 87,737,046	S1535P	probably benign	Het
C4b	A	G	17: 34,743,019		probably benign	Het
Ccdc157	A	G	11: 4,148,781	C242R	probably damaging	Het
Cep135	T	A	5: 76,593,347	M90K	possibly damaging	Het
Cfap36	A	T	11: 29,244,057		probably null	Het
Copb2	T	C	9: 98,581,150	S473P	probably damaging	Het
Cpb1	C	T	3: 20,251,954		probably null	Het
Cpsf1	A	G	15: 76,596,541	L1295P	probably damaging	Het
Dmp1	C	T	5: 104,212,462	Q335*	probably null	Het
Dyrk1a	T	A	16: 94,691,884	S621T	possibly damaging	Het
Exoc5	T	A	14: 49,034,964	Q331L	probably benign	Het
Fmnl1	G	A	11: 103,186,656	V287M	probably damaging	Het
Fras1	T	C	5: 96,709,891	S2015P	possibly damaging	Het
Gm7052	T	C	17: 22,040,004		probably benign	Het
Gprc5c	A	G	11: 114,864,252	I252V	probably benign	Het
Ints3	C	T	3: 90,394,322		probably null	Het
L1td1	A	G	4: 98,737,344	D592G	probably damaging	Het
Lamb3	A	G	1: 193,343,412	M1137V	probably benign	Het
Leng8	C	A	7: 4,145,482	A751E	probably benign	Het
Lfng	T	C	5: 140,612,535	V204A	probably damaging	Het
Lsm14b	A	G	2: 180,032,603	D233G	probably damaging	Het
Map4	C	T	9: 110,034,768	P354S	probably benign	Het
Mapt	G	A	11: 104,294,915	V53M	probably damaging	Het
Mier1	T	G	4: 103,155,541	S377A	possibly damaging	Het
Neurog1	T	C	13: 56,251,847	D29G	probably damaging	Het
Npr3	G	A	15: 11,895,789	A257V	probably damaging	Het
Nup188	T	C	2: 30,327,525	V824A	possibly damaging	Het
Olfm4	T	C	14: 80,021,310	S333P	probably damaging	Het
Olfr460	A	C	6: 40,572,252	I289L	probably damaging	Het
Olfr849	T	G	9: 19,441,815	F301V	probably benign	Het
Pbxip1	C	A	3: 89,443,590		probably benign	Het
Pde9a	G	T	17: 31,414,150	C38F	probably damaging	Het
Plb1	A	T	5: 32,342,544		probably benign	Het
Plcz1	T	C	6: 140,002,256		probably benign	Het
Plxnb1	T	C	9: 109,110,604	V1447A	probably damaging	Het
Pnldc1	A	T	17: 12,906,528	M73K	probably benign	Het
Psg20	C	T	7: 18,681,038	V311M	possibly damaging	Het
Psmd2	G	T	16: 20,659,405		probably null	Het
Rabgap1	T	C	2: 37,556,269	V859A	probably damaging	Het
Rad51b	T	A	12: 79,327,228	S194T	probably benign	Het
Rb1cc1	C	T	1: 6,248,771	Q788*	probably null	Het
Ror2	C	T	13: 53,111,617	G468R	probably damaging	Het
Slamf7	A	G	1: 171,641,186	I46T	possibly damaging	Het
Stab2	A	G	10: 86,922,895	S1060P	probably damaging	Het
Syndig1	T	A	2: 150,003,283	V242E	probably damaging	Het
Tgfbr3	G	A	5: 107,118,451	T801M	probably damaging	Het
Tmem132c	T	C	5: 127,359,552		probably benign	Het
Trav21-dv12	T	C	14: 53,876,731	Y103H	probably damaging	Het
Ubr3	T	C	2: 69,938,178	V443A	probably damaging	Het
Uhrf2	G	T	19: 30,092,120	C749F	probably damaging	Het
Ulk2	G	T	11: 61,791,436	S751*	probably null	Het
Wrn	G	A	8: 33,241,011	P1098S	possibly damaging	Het
Xrcc5	T	C	1: 72,346,349	V533A	possibly damaging	Het
Zc3h13	T	C	14: 75,309,723	S223P	probably damaging	Het
Zcchc11	T	C	4: 108,513,399	S871P	possibly damaging	Het

Other mutations in Chl1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00590:Chl1	APN	6	103693061	missense	probably benign	0.08
IGL00786:Chl1	APN	6	103675145	missense	probably damaging	1.00
IGL00959:Chl1	APN	6	103709250	splice site	probably null
IGL01109:Chl1	APN	6	103715393	missense	probably damaging	1.00
IGL01354:Chl1	APN	6	103665853	missense	probably benign	0.01
IGL01367:Chl1	APN	6	103729225	missense	probably benign	0.42
IGL01371:Chl1	APN	6	103715364	missense	probably damaging	1.00
IGL01724:Chl1	APN	6	103649573	missense	probably damaging	1.00
IGL02001:Chl1	APN	6	103642056	missense	possibly damaging	0.90
IGL02066:Chl1	APN	6	103698224	missense	probably benign	0.39
IGL02122:Chl1	APN	6	103675137	missense	probably benign	0.39
IGL02340:Chl1	APN	6	103698125	missense	probably damaging	1.00
IGL02420:Chl1	APN	6	103715369	missense	probably damaging	1.00
IGL02421:Chl1	APN	6	103717580	missense	probably damaging	1.00
IGL02429:Chl1	APN	6	103664809	unclassified	probably benign
IGL02825:Chl1	APN	6	103668803	missense	possibly damaging	0.87
IGL02858:Chl1	APN	6	103641988	missense	probably damaging	1.00
IGL03169:Chl1	APN	6	103665967	missense	probably damaging	1.00
IGL03185:Chl1	APN	6	103665863	missense	probably damaging	1.00
IGL03189:Chl1	APN	6	103683207	missense	possibly damaging	0.91
IGL03288:Chl1	APN	6	103675097	missense	probably damaging	1.00
IGL03404:Chl1	APN	6	103693091	missense	probably damaging	1.00
IGL03052:Chl1	UTSW	6	103691667	missense	probably benign	0.01
R0060:Chl1	UTSW	6	103711058	splice site	probably benign
R0060:Chl1	UTSW	6	103711058	splice site	probably benign
R0062:Chl1	UTSW	6	103749652	missense	unknown
R0314:Chl1	UTSW	6	103647301	missense	probably damaging	1.00
R0322:Chl1	UTSW	6	103701883	splice site	probably benign
R0685:Chl1	UTSW	6	103708542	splice site	probably null
R0702:Chl1	UTSW	6	103706622	missense	probably damaging	1.00
R1056:Chl1	UTSW	6	103675077	missense	possibly damaging	0.66
R1138:Chl1	UTSW	6	103693179	missense	probably benign	0.05
R1483:Chl1	UTSW	6	103647287	missense	probably damaging	1.00
R1571:Chl1	UTSW	6	103708484	missense	probably benign	0.34
R1620:Chl1	UTSW	6	103690242	missense	probably benign	0.00
R1645:Chl1	UTSW	6	103683180	missense	probably benign	0.06
R1773:Chl1	UTSW	6	103647331	critical splice donor site	probably null
R1852:Chl1	UTSW	6	103699159	splice site	probably null
R1891:Chl1	UTSW	6	103714583	missense	possibly damaging	0.88
R2146:Chl1	UTSW	6	103715401	critical splice donor site	probably null
R2147:Chl1	UTSW	6	103715401	critical splice donor site	probably null
R2148:Chl1	UTSW	6	103715401	critical splice donor site	probably null
R2163:Chl1	UTSW	6	103711231	missense	probably damaging	1.00
R2291:Chl1	UTSW	6	103715393	missense	probably damaging	1.00
R2920:Chl1	UTSW	6	103695343	missense	probably damaging	1.00
R3611:Chl1	UTSW	6	103698155	missense	probably damaging	1.00
R3979:Chl1	UTSW	6	103715284	nonsense	probably null
R4987:Chl1	UTSW	6	103674977	missense	probably damaging	1.00
R5266:Chl1	UTSW	6	103700543	missense	probably damaging	1.00
R5478:Chl1	UTSW	6	103683221	missense	probably damaging	1.00
R5523:Chl1	UTSW	6	103708714	missense	probably damaging	1.00
R5887:Chl1	UTSW	6	103717604	missense	probably benign	0.00
R5986:Chl1	UTSW	6	103709191	missense	probably benign	0.45
R6101:Chl1	UTSW	6	103693032	missense	probably damaging	0.96
R6179:Chl1	UTSW	6	103683243	missense	probably benign	0.38
R6366:Chl1	UTSW	6	103729236	missense	possibly damaging	0.95
R6634:Chl1	UTSW	6	103690259	missense	probably damaging	1.00
R6824:Chl1	UTSW	6	103714549	missense	probably damaging	1.00
R6913:Chl1	UTSW	6	103665948	nonsense	probably null
R7097:Chl1	UTSW	6	103706448	missense	probably damaging	1.00
R7122:Chl1	UTSW	6	103706448	missense	probably damaging	1.00
R7198:Chl1	UTSW	6	103706556	missense	probably damaging	1.00
R7203:Chl1	UTSW	6	103691674	missense	probably benign	0.13
R7527:Chl1	UTSW	6	103711201	missense	probably damaging	1.00
R7625:Chl1	UTSW	6	103729125	missense	probably damaging	1.00
R7667:Chl1	UTSW	6	103695495	missense	possibly damaging	0.82
R7683:Chl1	UTSW	6	103691652	missense	possibly damaging	0.72
R7712:Chl1	UTSW	6	103711102	missense	possibly damaging	0.94
R7838:Chl1	UTSW	6	103691674	missense	probably benign	0.01
R7863:Chl1	UTSW	6	103706514	missense	possibly damaging	0.46
R7874:Chl1	UTSW	6	103690263	missense	probably benign	0.22
R7998:Chl1	UTSW	6	103729289	missense	probably benign	0.01
R8044:Chl1	UTSW	6	103706632	missense	probably damaging	0.96
R8059:Chl1	UTSW	6	103674987	missense	probably damaging	0.97
R8462:Chl1	UTSW	6	103729169	missense	probably benign	0.11
R8558:Chl1	UTSW	6	103708429	missense	probably benign	0.14
R8827:Chl1	UTSW	6	103693150	missense	probably benign
R8865:Chl1	UTSW	6	103708861	missense	probably damaging	0.99
R8939:Chl1	UTSW	6	103665907	missense	probably damaging	1.00
R9092:Chl1	UTSW	6	103668854	unclassified	probably benign
Z1177:Chl1	UTSW	6	103693096	nonsense	probably null
Z1177:Chl1	UTSW	6	103697949	start gained	probably benign
Z1191:Chl1	UTSW	6	103683211	missense	probably damaging	1.00

Posted On

2013-12-09