Mutagenetix > Incidental Mutation

Incidental Mutation 'R2232:L1cam'

240145

Institutional Source

Beutler Lab

Gene Symbol

L1cam

Ensembl Gene

ENSMUSG00000031391

Gene Name

L1 cell adhesion molecule

Synonyms

L1-NCAM, NCAM-L1, L1, CD171

MMRRC Submission

040233-MU

Accession Numbers

Essential gene?

Possibly non essential (E-score: 0.277) question?

Stock #

R2232 (G1)

Quality Score

222

Status

Not validated

Chromosome

Chromosomal Location

72897384-72924843 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 72904947 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Asparagine to Isoleucine at position 503 (N503I)

Ref Sequence

ENSEMBL: ENSMUSP00000099935 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000066576] [ENSMUST00000102871] [ENSMUST00000114430] [ENSMUST00000146790]

AlphaFold

no structure available at present

Predicted Effect

possibly damaging
Transcript: ENSMUST00000066576
AA Change: N498I

PolyPhen 2 Score 0.948 (Sensitivity: 0.79; Specificity: 0.95)

SMART Domains

Protein: ENSMUSP00000068135
Gene: ENSMUSG00000031391
AA Change: N498I

Domain	Start	End	E-Value	Type
signal peptide	1	19	N/A	INTRINSIC
IGc2	43	115	3.59e-5	SMART
IG	137	224	2.66e-8	SMART
IGc2	249	313	1.25e-22	SMART
IGc2	339	405	1.06e-7	SMART
IGc2	433	498	6.55e-8	SMART
IGc2	524	592	1.19e-5	SMART
FN3	606	692	3.76e-6	SMART
FN3	709	791	1.31e-5	SMART
FN3	807	898	5.78e-7	SMART
FN3	912	996	1.51e-10	SMART
Blast:FN3	1010	1093	8e-36	BLAST
transmembrane domain	1118	1140	N/A	INTRINSIC
Pfam:Bravo_FIGEY	1141	1228	6.6e-32	PFAM

Predicted Effect

possibly damaging
Transcript: ENSMUST00000102871
AA Change: N503I

PolyPhen 2 Score 0.948 (Sensitivity: 0.79; Specificity: 0.95)

SMART Domains

Protein: ENSMUSP00000099935
Gene: ENSMUSG00000031391
AA Change: N503I

Domain	Start	End	E-Value	Type
signal peptide	1	19	N/A	INTRINSIC
IGc2	48	120	3.59e-5	SMART
IG	142	229	2.66e-8	SMART
IGc2	254	318	1.25e-22	SMART
IGc2	344	410	1.06e-7	SMART
IGc2	438	503	6.55e-8	SMART
IGc2	529	597	1.19e-5	SMART
FN3	611	697	3.76e-6	SMART
FN3	714	796	1.31e-5	SMART
FN3	812	903	5.78e-7	SMART
FN3	917	1001	1.51e-10	SMART
Blast:FN3	1015	1098	9e-36	BLAST
transmembrane domain	1123	1145	N/A	INTRINSIC
Pfam:Bravo_FIGEY	1146	1235	8.2e-30	PFAM

Predicted Effect

possibly damaging
Transcript: ENSMUST00000114430
AA Change: N503I

PolyPhen 2 Score 0.891 (Sensitivity: 0.82; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000110073
Gene: ENSMUSG00000031391
AA Change: N503I

Domain	Start	End	E-Value	Type
signal peptide	1	19	N/A	INTRINSIC
IGc2	48	120	3.59e-5	SMART
IG	142	229	2.66e-8	SMART
IGc2	254	318	1.25e-22	SMART
IGc2	344	410	1.06e-7	SMART
IGc2	438	503	6.55e-8	SMART
IGc2	529	597	1.19e-5	SMART
FN3	611	697	3.76e-6	SMART
FN3	714	796	1.31e-5	SMART
FN3	812	903	5.78e-7	SMART
FN3	917	1001	1.51e-10	SMART
Blast:FN3	1015	1098	9e-36	BLAST
transmembrane domain	1123	1145	N/A	INTRINSIC
Pfam:Bravo_FIGEY	1146	1233	6.7e-32	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000124560

SMART Domains

Protein: ENSMUSP00000115923
Gene: ENSMUSG00000031391

Domain	Start	End	E-Value	Type
Blast:FN3	2	34	2e-11	BLAST
Pfam:Bravo_FIGEY	42	121	9.7e-28	PFAM

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000129612

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000130110

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000135104

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000141221

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000144478

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000155246

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000145805

Predicted Effect

probably benign
Transcript: ENSMUST00000146790

SMART Domains

Protein: ENSMUSP00000121797
Gene: ENSMUSG00000031391

Domain	Start	End	E-Value	Type
signal peptide	1	19	N/A	INTRINSIC
Pfam:Ig_2	34	82	3.8e-7	PFAM
Pfam:I-set	35	84	1.7e-6	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000148250

SMART Domains

Protein: ENSMUSP00000114609
Gene: ENSMUSG00000031391

Domain	Start	End	E-Value	Type
IG	2	67	3.18e0	SMART
Pfam:fn3	137	190	6.5e-8	PFAM

Coding Region Coverage

1x: 99.1%
3x: 98.5%
10x: 97.1%
20x: 94.4%

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 an axonal glycoprotein belonging to the immunoglobulin supergene family. The ectodomain, consisting of several immunoglobulin-like domains and fibronectin-like repeats (type III), is linked via a single transmembrane sequence to a conserved cytoplasmic domain. This cell adhesion molecule plays an important role in nervous system development, including neuronal migration and differentiation. Mutations in the gene cause X-linked neurological syndromes known as CRASH (corpus callosum hypoplasia, retardation, aphasia, spastic paraplegia and hydrocephalus). Alternative splicing of this gene results in multiple transcript variants, some of which include an alternate exon that is considered to be specific to neurons. [provided by RefSeq, May 2013]
PHENOTYPE: Homozygous null mutants have reduced size, lessened sensitivity to touch and pain, weakness and incoordination of hind-legs, reduced corticospinal tract, impaired guidance of retinal and corticospinal axons, and in some cases, enlarged lateral ventricles. A hypomorphic line shows background effects. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 57 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Adam1a	A	C	5: 121,657,795 (GRCm39)	D499E	possibly damaging	Het
Adamtsl2	G	A	2: 26,993,190 (GRCm39)	G740E	probably damaging	Het
Adgrf4	C	T	17: 42,977,789 (GRCm39)	R518Q	possibly damaging	Het
Akap9	G	A	5: 4,096,603 (GRCm39)	V2493I	probably damaging	Het
Ankra2	T	C	13: 98,407,646 (GRCm39)	F199L	probably damaging	Het
Ankrd63	A	G	2: 118,533,846 (GRCm39)		probably benign	Het
Asns	A	G	6: 7,689,316 (GRCm39)	I62T	possibly damaging	Het
Celf3	T	A	3: 94,387,566 (GRCm39)		probably null	Het
Cyp4f37	A	G	17: 32,853,244 (GRCm39)	T403A	probably benign	Het
Dennd2b	T	C	7: 109,156,414 (GRCm39)	D112G	probably benign	Het
Dgkd	T	A	1: 87,857,464 (GRCm39)	S725R	probably benign	Het
Dnah5	G	A	15: 28,408,563 (GRCm39)		probably null	Het
Entrep2	G	A	7: 64,408,970 (GRCm39)	H475Y	probably damaging	Het
Ergic3	A	G	2: 155,859,736 (GRCm39)	T346A	probably damaging	Het
Fam227a	T	A	15: 79,499,582 (GRCm39)	Y591F	possibly damaging	Het
Gal3st1	T	C	11: 3,948,282 (GRCm39)	I163T	probably benign	Het
Ghrhr	T	C	6: 55,362,444 (GRCm39)	F347S	probably damaging	Het
Htr2a	A	T	14: 74,882,469 (GRCm39)	I152F	probably damaging	Het
Il17re	T	C	6: 113,441,761 (GRCm39)	C219R	probably damaging	Het
Kansl2	A	G	15: 98,422,359 (GRCm39)	L403S	probably damaging	Het
Kif21a	G	A	15: 90,869,565 (GRCm39)	Q429*	probably null	Het
Lrrk2	A	G	15: 91,648,919 (GRCm39)	K1638E	probably benign	Het
Mcpt9	A	T	14: 56,265,445 (GRCm39)	C85S	probably benign	Het
Mindy3	C	A	2: 12,408,856 (GRCm39)	R73M	probably benign	Het
Mrgprb3	T	C	7: 48,292,770 (GRCm39)	I260M	probably benign	Het
Nes	T	A	3: 87,886,238 (GRCm39)	I1499N	possibly damaging	Het
Ninl	A	G	2: 150,791,970 (GRCm39)	V851A	probably benign	Het
Oaz3	T	C	3: 94,341,846 (GRCm39)	T130A	probably benign	Het
Or10j7	A	G	1: 173,011,182 (GRCm39)	I273T	probably benign	Het
Or4c3d	A	T	2: 89,882,569 (GRCm39)	F33Y	probably benign	Het
Pacs2	G	A	12: 113,026,987 (GRCm39)	D605N	probably damaging	Het
Pcare	A	G	17: 72,056,279 (GRCm39)	S1133P	probably benign	Het
Pdk3	G	T	X: 92,857,604 (GRCm39)	N59K	probably damaging	Het
Pigq	T	C	17: 26,151,183 (GRCm39)	H322R	probably benign	Het
Ppp3r1	G	A	11: 17,143,115 (GRCm39)	G68R	probably damaging	Het
Proz	A	G	8: 13,113,356 (GRCm39)	Y59C	probably damaging	Het
Prpf39	C	T	12: 65,090,786 (GRCm39)	R32*	probably null	Het
Prr5	T	C	15: 84,586,981 (GRCm39)	S244P	probably benign	Het
Pth2r	G	T	1: 65,375,928 (GRCm39)	W62L	probably damaging	Het
Scin	T	A	12: 40,118,930 (GRCm39)	K622I	probably damaging	Het
Serpinb6a	T	C	13: 34,109,303 (GRCm39)	K143R	probably damaging	Het
Ska1	G	T	18: 74,330,137 (GRCm39)		probably null	Het
Slc30a8	G	T	15: 52,169,960 (GRCm39)	R62S	probably benign	Het
Slc8a3	A	C	12: 81,361,994 (GRCm39)	I275S	probably damaging	Het
Sp2	C	T	11: 96,846,762 (GRCm39)	C527Y	probably damaging	Het
Spmap2l	A	G	5: 77,207,252 (GRCm39)	I337V	possibly damaging	Het
Sspo	A	G	6: 48,425,606 (GRCm39)	I76V	probably damaging	Het
Sult1c2	G	T	17: 54,138,848 (GRCm39)	T243K	probably benign	Het
Svil	T	A	18: 5,046,640 (GRCm39)	M1K	probably null	Het
Tet3	T	C	6: 83,346,453 (GRCm39)	D1328G	probably damaging	Het
Tnfsf14	T	C	17: 57,500,876 (GRCm39)	D65G	probably benign	Het
Trmt9b	T	A	8: 36,979,707 (GRCm39)	C437S	probably damaging	Het
Ttc3	T	C	16: 94,260,831 (GRCm39)	S1439P	probably benign	Het
Ttn	A	T	2: 76,774,497 (GRCm39)	F2136L	probably damaging	Het
Usb1	T	G	8: 96,070,674 (GRCm39)	L200R	probably damaging	Het
Usp20	A	G	2: 30,908,750 (GRCm39)	N777S	probably benign	Het
Zfp92	G	T	X: 72,466,358 (GRCm39)	L450F	possibly damaging	Het

Other mutations in L1cam

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01712:L1cam	APN	X	72,908,044 (GRCm39)	missense	probably damaging	1.00
IGL02074:L1cam	APN	X	72,906,619 (GRCm39)	missense	probably damaging	1.00
IGL03059:L1cam	APN	X	72,910,630 (GRCm39)	missense	probably benign	0.01
IGL03351:L1cam	APN	X	72,906,634 (GRCm39)	missense	probably damaging	1.00
R0079:L1cam	UTSW	X	72,913,364 (GRCm39)	missense	probably damaging	0.99
R2146:L1cam	UTSW	X	72,904,747 (GRCm39)	missense	probably damaging	1.00
R2148:L1cam	UTSW	X	72,904,747 (GRCm39)	missense	probably damaging	1.00
R2231:L1cam	UTSW	X	72,904,947 (GRCm39)	missense	possibly damaging	0.95

Predicted Primers

PCR Primer
(F):5'- GTGAATGTCACCCTTGCACC -3'
(R):5'- CTCATCTAAAGATCCCAGGAGG -3'

Sequencing Primer
(F):5'- TCTTCTCAATTGCGCTCCGG -3'
(R):5'- GCATGGAGTCCAAGTTGGTTAGTC -3'

Posted On

2014-10-15