Incidental Mutation 'IGL01712:L1cam'
ID 104827
Institutional Source Australian Phenomics Network (link to record)
Gene Symbol L1cam
Ensembl Gene ENSMUSG00000031391
Gene Name L1 cell adhesion molecule
Synonyms L1-NCAM, NCAM-L1, L1, CD171
Accession Numbers
Essential gene? Possibly non essential (E-score: 0.277) question?
Stock # IGL01712
Quality Score
Status
Chromosome X
Chromosomal Location 72897384-72924843 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 72908044 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Tyrosine to Cysteine at position 169 (Y169C)
Ref Sequence ENSEMBL: ENSMUSP00000110073 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000066576] [ENSMUST00000102871] [ENSMUST00000114430] [ENSMUST00000146790]
AlphaFold no structure available at present
Predicted Effect probably damaging
Transcript: ENSMUST00000066576
AA Change: Y164C

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000068135
Gene: ENSMUSG00000031391
AA Change: Y164C

DomainStartEndE-ValueType
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 probably damaging
Transcript: ENSMUST00000102871
AA Change: Y169C

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000099935
Gene: ENSMUSG00000031391
AA Change: Y169C

DomainStartEndE-ValueType
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 probably damaging
Transcript: ENSMUST00000114430
AA Change: Y169C

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000110073
Gene: ENSMUSG00000031391
AA Change: Y169C

DomainStartEndE-ValueType
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 noncoding transcript
Transcript: ENSMUST00000129612
Predicted Effect noncoding transcript
Transcript: ENSMUST00000141221
Predicted Effect probably benign
Transcript: ENSMUST00000146790
SMART Domains Protein: ENSMUSP00000121797
Gene: ENSMUSG00000031391

DomainStartEndE-ValueType
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

DomainStartEndE-ValueType
IG 2 67 3.18e0 SMART
Pfam:fn3 137 190 6.5e-8 PFAM
Predicted Effect noncoding transcript
Transcript: ENSMUST00000155246
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 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: 48 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Aadacl2fm3 T A 3: 59,776,321 (GRCm39) I164N possibly damaging Het
Adgrb3 A G 1: 25,865,360 (GRCm39) V161A probably benign Het
Arhgdib G A 6: 136,901,195 (GRCm39) T178M probably damaging Het
Atp11a T A 8: 12,901,138 (GRCm39) I989K probably benign Het
Bcam T C 7: 19,492,692 (GRCm39) S498G probably damaging Het
Bcas3 A G 11: 85,471,874 (GRCm39) I728V probably damaging Het
Cep57 G T 9: 13,724,713 (GRCm39) P119Q possibly damaging Het
Cimip2a T C 2: 25,108,804 (GRCm39) probably benign Het
Clip4 T A 17: 72,106,036 (GRCm39) I73N probably damaging Het
Cpa4 A G 6: 30,590,815 (GRCm39) D371G possibly damaging Het
Dnah7a A G 1: 53,462,429 (GRCm39) S3721P probably benign Het
Fcrla T C 1: 170,749,192 (GRCm39) probably null Het
Foxg1 T C 12: 49,432,403 (GRCm39) S379P possibly damaging Het
Gatm T A 2: 122,431,306 (GRCm39) Y227F possibly damaging Het
Grid2 A T 6: 64,642,899 (GRCm39) D887V possibly damaging Het
Gtpbp6 A T 5: 110,252,245 (GRCm39) I429N probably benign Het
Ighmbp2 A G 19: 3,323,038 (GRCm39) probably benign Het
Irs4 T C X: 140,505,395 (GRCm39) N934D unknown Het
Kif16b T A 2: 142,490,391 (GRCm39) N1257I probably damaging Het
L3mbtl3 A T 10: 26,152,133 (GRCm39) M821K probably damaging Het
Lig3 A G 11: 82,680,367 (GRCm39) probably benign Het
Lpin2 T A 17: 71,522,063 (GRCm39) D32E probably damaging Het
Mcoln3 T C 3: 145,834,019 (GRCm39) probably benign Het
Mgst2 T C 3: 51,571,992 (GRCm39) V40A probably damaging Het
Mov10l1 T C 15: 88,908,969 (GRCm39) S997P probably damaging Het
Mycbpap G T 11: 94,403,481 (GRCm39) H187Q possibly damaging Het
Onecut2 T A 18: 64,519,673 (GRCm39) S478T probably damaging Het
Or2n1d A T 17: 38,646,848 (GRCm39) T267S probably benign Het
Or52h7 T C 7: 104,214,226 (GRCm39) V266A probably benign Het
Pcdhb5 A T 18: 37,454,306 (GRCm39) I229F probably damaging Het
Pfas A G 11: 68,881,886 (GRCm39) V933A probably benign Het
Phldb2 A T 16: 45,571,792 (GRCm39) I1200N probably damaging Het
Pla2g4e C A 2: 120,019,884 (GRCm39) probably null Het
Prr36 G A 8: 4,265,243 (GRCm39) P169L probably damaging Het
Rhot2 A G 17: 26,060,334 (GRCm39) probably null Het
Serpina3f C T 12: 104,184,657 (GRCm39) P267L probably damaging Het
Sppl2a C T 2: 126,746,823 (GRCm39) probably benign Het
Tas2r122 A T 6: 132,688,725 (GRCm39) M56K possibly damaging Het
Tbxas1 A G 6: 39,057,994 (GRCm39) T450A probably benign Het
Tex16 T C X: 111,003,451 (GRCm39) S87P probably damaging Het
Them7 T A 2: 105,209,230 (GRCm39) F183L possibly damaging Het
Tmbim7 A G 5: 3,720,074 (GRCm39) T116A probably damaging Het
Tomm40 G T 7: 19,437,288 (GRCm39) S224R probably benign Het
Top3a A T 11: 60,652,562 (GRCm39) I84N probably damaging Het
Vmn1r28 A G 6: 58,242,393 (GRCm39) T79A probably benign Het
Vmn2r61 A T 7: 41,909,661 (GRCm39) Y62F probably damaging Het
Zbtb42 T C 12: 112,646,718 (GRCm39) C298R probably benign Het
Zfp395 G A 14: 65,623,836 (GRCm39) E102K probably damaging Het
Other mutations in L1cam
AlleleSourceChrCoordTypePredicted EffectPPH Score
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
R2232:L1cam UTSW X 72,904,947 (GRCm39) missense possibly damaging 0.95
Posted On 2014-01-21