Mutagenetix > Incidental Mutation

Incidental Mutation 'R2920:Chl1'

255467

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

040505-MU

Accession Numbers

Essential gene?

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

Stock #

R2920 (G1)

Quality Score

213

Status

Validated

Chromosome

Chromosomal Location

103487372-103709999 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

C to A at 103672304 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Threonine to Lysine at position 531 (T531K)

Ref Sequence

ENSEMBL: ENSMUSP00000145026 (fasta)

Gene Model

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

AlphaFold

P70232

Predicted Effect

probably damaging
Transcript: ENSMUST00000066905
AA Change: T515K

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000063933
Gene: ENSMUSG00000030077
AA Change: T515K

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: ENSMUST00000203830
AA Change: T515K

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000144758
Gene: ENSMUSG00000030077
AA Change: T515K

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: T531K

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000145026
Gene: ENSMUSG00000030077
AA Change: T531K

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

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

Meta Mutation Damage Score

0.6341

Coding Region Coverage

1x: 99.1%
3x: 98.6%
10x: 97.3%
20x: 95.0%

Validation Efficiency

96% (48/50)

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: 47 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Adgb	A	G	10: 10,265,987 (GRCm39)	Y1025H	probably damaging	Het
Adgrv1	C	T	13: 81,596,984 (GRCm39)	A4122T	probably benign	Het
Aloxe3	C	T	11: 69,033,749 (GRCm39)	T621I	probably damaging	Het
Atp2b3	A	C	X: 72,577,526 (GRCm39)	T318P	probably benign	Het
Atrx	A	T	X: 104,874,474 (GRCm39)	V1962D	probably benign	Het
Clca3b	T	A	3: 144,543,614 (GRCm39)	D405V	probably benign	Het
Clca3b	C	T	3: 144,552,692 (GRCm39)	D115N	probably benign	Het
Comtd1	A	G	14: 21,897,686 (GRCm39)	L149P	possibly damaging	Het
Cops7a	A	G	6: 124,939,325 (GRCm39)	V108A	probably benign	Het
Crebbp	A	G	16: 3,936,946 (GRCm39)	V343A	probably damaging	Het
Edrf1	T	A	7: 133,269,301 (GRCm39)	D1109E	probably benign	Het
Elmo3	A	G	8: 106,034,691 (GRCm39)	E359G	possibly damaging	Het
Ep400	C	A	5: 110,903,780 (GRCm39)	G273V	probably damaging	Het
Fgfr3	A	G	5: 33,891,284 (GRCm39)	N516S	probably damaging	Het
Glb1l	T	A	1: 75,185,834 (GRCm39)	E31D	probably benign	Het
Hdac1-ps	A	G	17: 78,800,275 (GRCm39)	D422G	probably damaging	Het
Il12rb2	C	T	6: 67,337,552 (GRCm39)	V110I	probably damaging	Het
Ints3	T	C	3: 90,300,469 (GRCm39)	E884G	probably benign	Het
Lin7b	A	G	7: 45,017,821 (GRCm39)	V170A	possibly damaging	Het
Lrch2	A	T	X: 146,256,026 (GRCm39)	V750E	probably damaging	Het
Mepe	C	T	5: 104,486,113 (GRCm39)	R418C	probably damaging	Het
Mettl25	A	T	10: 105,601,038 (GRCm39)		probably null	Het
Mphosph9	G	A	5: 124,399,069 (GRCm39)	T982I	probably benign	Het
Mslnl	G	A	17: 25,961,908 (GRCm39)	V128M	probably damaging	Het
Myo10	G	T	15: 25,801,226 (GRCm39)	V1472L	probably damaging	Het
Myo9b	A	G	8: 71,778,501 (GRCm39)	K445R	probably damaging	Het
Ntng2	T	C	2: 29,094,223 (GRCm39)	M383V	probably benign	Het
Or13n4	C	T	7: 106,423,571 (GRCm39)	R54Q	probably benign	Het
Or2z2	T	C	11: 58,346,403 (GRCm39)	Y124C	probably damaging	Het
Or7a37	A	C	10: 78,805,846 (GRCm39)	D121A	probably damaging	Het
Pak6	A	T	2: 118,524,488 (GRCm39)		probably benign	Het
Pcdh8	G	T	14: 80,006,154 (GRCm39)	P803Q	possibly damaging	Het
Pfkfb3	C	T	2: 11,489,138 (GRCm39)	V286I	probably benign	Het
Rbp3	C	T	14: 33,677,975 (GRCm39)	T641M	probably damaging	Het
Rint1	A	G	5: 24,010,400 (GRCm39)	E203G	probably benign	Het
Sdf2	G	C	11: 78,145,680 (GRCm39)	V126L	probably damaging	Het
Slc13a5	T	C	11: 72,138,617 (GRCm39)	E442G	possibly damaging	Het
Slc14a2	G	T	18: 78,201,512 (GRCm39)	S669*	probably null	Het
Slc38a7	A	G	8: 96,572,571 (GRCm39)	I157T	possibly damaging	Het
Slc4a5	T	C	6: 83,241,369 (GRCm39)	L215P	probably damaging	Het
Tbc1d9	T	C	8: 83,937,098 (GRCm39)	V60A	probably benign	Het
Tcerg1l	T	C	7: 137,850,108 (GRCm39)	R422G	probably damaging	Het
Tmem107	T	C	11: 68,962,247 (GRCm39)	L68P	probably damaging	Het
Ugt2b5	A	G	5: 87,273,266 (GRCm39)	F467L	possibly damaging	Het
Vmn1r19	A	T	6: 57,381,909 (GRCm39)	N154I	probably benign	Het
Vmn2r69	T	A	7: 85,060,973 (GRCm39)	I204L	probably benign	Het
Zbtb1	T	A	12: 76,432,619 (GRCm39)	S202T	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
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
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'- GGTGCATGCACTTAAATTTTCTCGG -3'
(R):5'- AGGACCACTTCTCTAATGTGATC -3'

Sequencing Primer
(F):5'- TCTCGGGTTCAATGGTAGAATATAG -3'
(R):5'- CACACGTCTTTTCACAGCAG -3'

Posted On

2014-12-29