Mutagenetix > Incidental Mutation

Incidental Mutation 'IGL02420:Chl1'

292634

Institutional Source

Australian Phenomics Network (link to record)

Gene Symbol

Chl1

Ensembl Gene

ENSMUSG00000030077

Gene Name

cell adhesion molecule L1-like

Synonyms

A530023M13Rik, close homolog of L1, LICAM2, CALL

Accession Numbers

Essential gene?

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

Stock #

IGL02420

Quality Score

Status

Chromosome

Chromosomal Location

103487372-103709999 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

G to A at 103692330 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Valine to Methionine at position 1066 (V1066M)

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: V1104M

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

SMART Domains

Protein: ENSMUSP00000063933
Gene: ENSMUSG00000030077
AA Change: V1104M

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: V1104M

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

SMART Domains

Protein: ENSMUSP00000144758
Gene: ENSMUSG00000030077
AA Change: V1104M

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: V1066M

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

SMART Domains

Protein: ENSMUSP00000145026
Gene: ENSMUSG00000030077
AA Change: V1066M

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: ENSMUST00000205098
AA Change: V323M

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

SMART Domains

Protein: ENSMUSP00000144739
Gene: ENSMUSG00000030077
AA Change: V323M

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: 46 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Acsbg3	A	G	17: 57,187,494 (GRCm39)	N136S	probably damaging	Het
Adcy8	A	G	15: 64,659,303 (GRCm39)	S496P	probably damaging	Het
Agbl3	T	A	6: 34,762,242 (GRCm39)	S81T	possibly damaging	Het
Apobec1	A	T	6: 122,558,531 (GRCm39)	Y75N	probably benign	Het
Asic2	A	G	11: 80,772,479 (GRCm39)	L517P	probably benign	Het
Atp8a1	A	G	5: 67,840,126 (GRCm39)	S752P	probably damaging	Het
Blm	T	C	7: 80,145,754 (GRCm39)	Y775C	probably damaging	Het
C1qtnf5	T	C	9: 44,019,901 (GRCm39)	I175T	probably benign	Het
Ccdc81	G	A	7: 89,524,946 (GRCm39)	T545I	probably benign	Het
Ccdc88b	T	C	19: 6,834,317 (GRCm39)	E174G	probably damaging	Het
Cntn6	T	A	6: 104,823,103 (GRCm39)		probably null	Het
Csgalnact1	C	A	8: 68,854,144 (GRCm39)	G219V	probably damaging	Het
Cyren	T	C	6: 34,851,404 (GRCm39)	Y150C	probably damaging	Het
Cysrt1	T	C	2: 25,129,360 (GRCm39)	I51V	probably benign	Het
Dnah7a	T	C	1: 53,725,702 (GRCm39)	N69S	probably benign	Het
Fam83d	T	C	2: 158,627,655 (GRCm39)	L448P	probably benign	Het
Gm9631	G	A	11: 121,834,478 (GRCm39)			Het
Hmcn1	T	C	1: 150,598,175 (GRCm39)	Y1709C	probably damaging	Het
Inppl1	G	A	7: 101,481,526 (GRCm39)		probably benign	Het
Iqcc	T	C	4: 129,510,748 (GRCm39)	T256A	probably benign	Het
Itprid2	T	C	2: 79,465,986 (GRCm39)	S35P	probably damaging	Het
Lyst	G	A	13: 13,835,541 (GRCm39)	C1741Y	probably benign	Het
Lyz1	A	T	10: 117,124,535 (GRCm39)	C134S	probably damaging	Het
Mpzl3	T	C	9: 44,977,815 (GRCm39)	I141T	possibly damaging	Het
Mterf1a	T	C	5: 3,941,047 (GRCm39)	N274D	probably damaging	Het
Myo18a	T	A	11: 77,709,519 (GRCm39)	V543D	possibly damaging	Het
Myo18b	A	T	5: 112,975,852 (GRCm39)	D1332E	possibly damaging	Het
Or2r11	A	G	6: 42,437,110 (GRCm39)	V281A	probably benign	Het
Pcdh15	A	T	10: 74,138,938 (GRCm39)	D333V	probably damaging	Het
Plekha7	A	G	7: 115,757,469 (GRCm39)	Y494H	probably damaging	Het
Plekhg1	A	G	10: 3,914,106 (GRCm39)	N1276S	probably damaging	Het
Ppig	T	C	2: 69,562,571 (GRCm39)	V5A	probably benign	Het
Prag1	A	T	8: 36,614,580 (GRCm39)		probably benign	Het
Prom1	T	C	5: 44,220,496 (GRCm39)	N84S	probably benign	Het
Ptprh	T	A	7: 4,583,929 (GRCm39)	Y221F	probably damaging	Het
Qsox2	A	G	2: 26,110,731 (GRCm39)	Y162H	probably benign	Het
Rab2a	C	T	4: 8,572,553 (GRCm39)	T49M	possibly damaging	Het
Ring1	A	G	17: 34,242,122 (GRCm39)	S96P	possibly damaging	Het
Ripk3	A	G	14: 56,022,691 (GRCm39)	F411S	probably benign	Het
Rock1	T	C	18: 10,070,619 (GRCm39)		probably null	Het
Rtn4rl1	A	G	11: 75,156,645 (GRCm39)	N359S	probably damaging	Het
Sufu	A	G	19: 46,413,481 (GRCm39)	T76A	probably damaging	Het
Sugct	C	A	13: 17,627,053 (GRCm39)	V267F	probably damaging	Het
Tcf4	A	T	18: 69,697,210 (GRCm39)	R29W	probably damaging	Het
Tnfsf18	A	T	1: 161,331,158 (GRCm39)	I103L	probably benign	Het
Vwf	A	G	6: 125,654,879 (GRCm39)	E2525G	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
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
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

Posted On

2015-04-16