Mutagenetix > Incidental Mutation

Incidental Mutation 'IGL02421:Chl1'

292677

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 #

IGL02421

Quality Score

Status

Chromosome

Chromosomal Location

103487372-103709999 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to T at 103694541 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Histidine to Leucine at position 1121 (H1121L)

Ref Sequence

ENSEMBL: ENSMUSP00000144758 (fasta)

Gene Model

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

AlphaFold

P70232

Predicted Effect

probably damaging
Transcript: ENSMUST00000066905
AA Change: H1121L

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

SMART Domains

Protein: ENSMUSP00000063933
Gene: ENSMUSG00000030077
AA Change: H1121L

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: H1121L

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

SMART Domains

Protein: ENSMUSP00000144758
Gene: ENSMUSG00000030077
AA Change: H1121L

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: H1083L

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

SMART Domains

Protein: ENSMUSP00000145026
Gene: ENSMUSG00000030077
AA Change: H1083L

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: H340L

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

SMART Domains

Protein: ENSMUSP00000144739
Gene: ENSMUSG00000030077
AA Change: H340L

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: 45 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
a	T	C	2: 154,892,672 (GRCm39)	F117S	probably damaging	Het
A930011G23Rik	A	G	5: 99,377,236 (GRCm39)	S404P	probably damaging	Het
A930011G23Rik	G	A	5: 99,377,241 (GRCm39)	P402L	probably damaging	Het
Acacb	A	G	5: 114,361,939 (GRCm39)	T1394A	probably benign	Het
Adam19	A	G	11: 46,028,380 (GRCm39)	N671S	probably damaging	Het
Akap13	A	T	7: 75,367,554 (GRCm39)	N1815I	possibly damaging	Het
Aloxe3	A	G	11: 69,020,872 (GRCm39)	D199G	possibly damaging	Het
Ap1g2	G	A	14: 55,339,859 (GRCm39)	A440V	probably damaging	Het
Bmt2	G	T	6: 13,628,841 (GRCm39)	Q281K	probably damaging	Het
Celsr3	T	C	9: 108,717,662 (GRCm39)	F2243L	probably damaging	Het
Cenpb	G	A	2: 131,021,601 (GRCm39)	R66C	probably damaging	Het
Cpb1	T	C	3: 20,306,148 (GRCm39)	Y344C	probably damaging	Het
Cspg5	T	A	9: 110,076,460 (GRCm39)		probably benign	Het
Dnah11	T	C	12: 118,150,637 (GRCm39)	N374D	probably damaging	Het
Dnah3	A	G	7: 119,550,215 (GRCm39)	V3368A	possibly damaging	Het
Eml4	T	C	17: 83,785,321 (GRCm39)	S829P	probably benign	Het
Got2-ps1	T	C	5: 138,362,811 (GRCm39)		noncoding transcript	Het
Hal	T	C	10: 93,339,335 (GRCm39)	C475R	probably damaging	Het
Mapkbp1	C	T	2: 119,850,136 (GRCm39)	P806S	possibly damaging	Het
Mmrn1	A	T	6: 60,921,806 (GRCm39)	T88S	probably benign	Het
Napsa	A	G	7: 44,234,479 (GRCm39)	H237R	probably damaging	Het
Opn5	C	T	17: 42,907,446 (GRCm39)		probably benign	Het
Or1d2	T	C	11: 74,256,017 (GRCm39)	I174T	probably damaging	Het
Or4c110	T	C	2: 88,831,688 (GRCm39)		probably null	Het
Or51f2	T	C	7: 102,526,966 (GRCm39)	I213T	probably damaging	Het
Or56b2	A	G	7: 104,337,740 (GRCm39)	N173D	probably benign	Het
Pira12	T	C	7: 3,899,994 (GRCm39)	N203D	possibly damaging	Het
Polb	C	T	8: 23,130,389 (GRCm39)	G179D	probably damaging	Het
Primpol	G	T	8: 47,060,830 (GRCm39)		probably benign	Het
Prom2	T	A	2: 127,373,802 (GRCm39)		probably null	Het
Psmb10	A	G	8: 106,664,124 (GRCm39)		probably null	Het
Ranbp2	T	G	10: 58,316,376 (GRCm39)	S2365R	probably damaging	Het
Sgce	G	A	6: 4,694,187 (GRCm39)		probably benign	Het
Slc25a34	A	G	4: 141,348,753 (GRCm39)	V237A	probably benign	Het
Slc39a2	A	T	14: 52,131,329 (GRCm39)	T25S	probably benign	Het
Smarca4	T	C	9: 21,550,535 (GRCm39)	C423R	probably damaging	Het
Stt3b	G	A	9: 115,080,920 (GRCm39)		probably benign	Het
Tbl1xr1	A	T	3: 22,257,327 (GRCm39)	I397F	probably damaging	Het
Tie1	A	G	4: 118,343,591 (GRCm39)	V117A	probably damaging	Het
Tmc3	T	C	7: 83,271,952 (GRCm39)	F1035L	probably benign	Het
Trhde	T	A	10: 114,248,366 (GRCm39)	K944N	probably damaging	Het
Vmn1r54	G	A	6: 90,246,133 (GRCm39)	A16T	probably benign	Het
Washc4	T	A	10: 83,415,414 (GRCm39)	N801K	probably damaging	Het
Xylt2	A	G	11: 94,558,588 (GRCm39)	Y523H	possibly damaging	Het
Znfx1	T	C	2: 166,902,000 (GRCm39)	R5G	probably 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
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