Mutagenetix > Incidental Mutation

Incidental Mutation 'R0314:Chl1'

25370

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

038524-MU

Accession Numbers

Essential gene?

Possibly non essential (E-score: 0.458) question?

Stock #

R0314 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

103487372-103709999 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 103624262 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Cysteine to Serine at position 57 (C57S)

Ref Sequence

ENSEMBL: ENSMUSP00000144725 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000066905] [ENSMUST00000203830] [ENSMUST00000203912] [ENSMUST00000204321]

AlphaFold

P70232

Predicted Effect

probably damaging
Transcript: ENSMUST00000066905
AA Change: C57S

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

SMART Domains

Protein: ENSMUSP00000063933
Gene: ENSMUSG00000030077
AA Change: C57S

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

noncoding transcript
Transcript: ENSMUST00000203489

Predicted Effect

probably damaging
Transcript: ENSMUST00000203830
AA Change: C57S

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

SMART Domains

Protein: ENSMUSP00000144758
Gene: ENSMUSG00000030077
AA Change: C57S

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 damaging
Transcript: ENSMUST00000203912
AA Change: C57S

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

SMART Domains

Protein: ENSMUSP00000145026
Gene: ENSMUSG00000030077
AA Change: C57S

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 damaging
Transcript: ENSMUST00000204321
AA Change: C57S

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000144725
Gene: ENSMUSG00000030077
AA Change: C57S

Domain	Start	End	E-Value	Type
signal peptide	1	25	N/A	INTRINSIC
IG_like	48	116	1.3e-4	SMART

Meta Mutation Damage Score

0.8567

Coding Region Coverage

1x: 98.9%
3x: 97.8%
10x: 94.9%
20x: 88.7%

Validation Efficiency

100% (41/41)

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: 39 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Arih2	T	C	9: 108,485,878 (GRCm39)	N345D	probably damaging	Het
Ascc3	C	T	10: 50,514,095 (GRCm39)	S298L	possibly damaging	Het
Cacna1e	A	G	1: 154,317,997 (GRCm39)	Y1462H	probably damaging	Het
Car9	T	C	4: 43,509,212 (GRCm39)		probably null	Het
Cenpc1	A	T	5: 86,185,230 (GRCm39)	M427K	probably benign	Het
Cntn3	T	C	6: 102,397,342 (GRCm39)	Y77C	probably damaging	Het
Cobll1	T	C	2: 64,919,865 (GRCm39)	K1187E	possibly damaging	Het
Fkbpl	C	T	17: 34,865,026 (GRCm39)	H265Y	possibly damaging	Het
Fmo1	T	G	1: 162,687,031 (GRCm39)	E32A	probably damaging	Het
Fnip2	G	A	3: 79,388,496 (GRCm39)	T715I	probably damaging	Het
Fzd6	T	A	15: 38,889,128 (GRCm39)	I82K	possibly damaging	Het
Grm5	T	C	7: 87,252,163 (GRCm39)	S138P	probably damaging	Het
Klra5	T	C	6: 129,880,553 (GRCm39)	Y115C	probably damaging	Het
Lgr4	T	C	2: 109,821,438 (GRCm39)		probably benign	Het
Limd1	T	G	9: 123,345,892 (GRCm39)	I557S	probably benign	Het
Mpv17l	A	T	16: 13,758,863 (GRCm39)	I96L	probably benign	Het
Neb	A	T	2: 52,133,343 (GRCm39)	D3398E	probably benign	Het
Nup155	T	C	15: 8,176,736 (GRCm39)	S1005P	probably benign	Het
Or2v2	A	T	11: 49,004,519 (GRCm39)	D11E	possibly damaging	Het
Or52a5b	T	C	7: 103,417,388 (GRCm39)	D72G	probably damaging	Het
Pebp4	G	T	14: 70,297,103 (GRCm39)	S214I	possibly damaging	Het
Pex26	T	C	6: 121,161,443 (GRCm39)		probably null	Het
Rbbp8	A	T	18: 11,848,875 (GRCm39)	Q230L	probably benign	Het
Rif1	GCCACCA	GCCA	2: 52,000,336 (GRCm39)		probably benign	Het
Robo2	G	A	16: 73,753,525 (GRCm39)	T784M	probably damaging	Het
Slc5a1	T	C	5: 33,303,995 (GRCm39)	I270T	probably benign	Het
Spag4	C	T	2: 155,909,229 (GRCm39)		probably benign	Het
Stt3a	T	C	9: 36,660,841 (GRCm39)		probably benign	Het
Svep1	C	T	4: 58,096,331 (GRCm39)	E1430K	possibly damaging	Het
Timd5	G	A	11: 46,419,364 (GRCm39)	C60Y	probably damaging	Het
Uba6	A	T	5: 86,265,946 (GRCm39)	V956E	probably damaging	Het
Ube2j1	T	A	4: 33,043,991 (GRCm39)		probably benign	Het
Ubr5	A	G	15: 37,997,431 (GRCm39)	S1741P	probably damaging	Het
Vmn2r1	A	G	3: 63,993,980 (GRCm39)	T109A	probably damaging	Het
Vmn2r60	T	C	7: 41,784,985 (GRCm39)		probably benign	Het
Vstm2a	A	G	11: 16,318,388 (GRCm39)		probably benign	Het
Zdhhc20	T	A	14: 58,094,076 (GRCm39)	K195N	probably damaging	Het
Zfp683	A	G	4: 133,786,052 (GRCm39)	Y393C	probably benign	Het
Zzz3	T	C	3: 152,133,085 (GRCm39)	S48P	probably benign	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
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
R1852:Chl1	UTSW	6	103,676,120 (GRCm39)	splice 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

PCR Primer
(F):5'- gacactgaacataaactatcacaCTTACCGA -3'
(R):5'- cacacacacacacTCAAGCAAACTC -3'

Sequencing Primer
(F):5'- ctatcacaCTTACCGATGTAGAATAC -3'
(R):5'- AAAGAAGTACACAGTTAAGTTCTACC -3'

Posted On

2013-04-16