Incidental Mutation 'IGL00590:Chl1'
ID 5396
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 # IGL00590
Quality Score
Status
Chromosome 6
Chromosomal Location 103487372-103709999 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 103670022 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Tyrosine to Histidine at position 471 (Y471H)
Ref Sequence ENSEMBL: ENSMUSP00000144758 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000066905] [ENSMUST00000203830] [ENSMUST00000203912] [ENSMUST00000205098]
AlphaFold P70232
Predicted Effect probably benign
Transcript: ENSMUST00000066905
AA Change: Y471H

PolyPhen 2 Score 0.080 (Sensitivity: 0.93; Specificity: 0.85)
SMART Domains Protein: ENSMUSP00000063933
Gene: ENSMUSG00000030077
AA Change: Y471H

DomainStartEndE-ValueType
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 benign
Transcript: ENSMUST00000203830
AA Change: Y471H

PolyPhen 2 Score 0.080 (Sensitivity: 0.93; Specificity: 0.85)
SMART Domains Protein: ENSMUSP00000144758
Gene: ENSMUSG00000030077
AA Change: Y471H

DomainStartEndE-ValueType
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 benign
Transcript: ENSMUST00000203912
AA Change: Y487H

PolyPhen 2 Score 0.058 (Sensitivity: 0.94; Specificity: 0.84)
SMART Domains Protein: ENSMUSP00000145026
Gene: ENSMUSG00000030077
AA Change: Y487H

DomainStartEndE-ValueType
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

DomainStartEndE-ValueType
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: 33 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abca16 T G 7: 120,023,038 (GRCm39) F58C probably damaging Het
Adgrf5 G T 17: 43,764,038 (GRCm39) G1320V probably damaging Het
Akap13 A G 7: 75,260,417 (GRCm39) K211E probably benign Het
Akap8l T C 17: 32,552,071 (GRCm39) D402G possibly damaging Het
Akna T C 4: 63,290,115 (GRCm39) I1198V probably benign Het
Apaf1 T A 10: 90,859,650 (GRCm39) I832F probably damaging Het
Cbl A C 9: 44,112,495 (GRCm39) L67V probably damaging Het
Cystm1 T A 18: 36,499,728 (GRCm39) Y48N unknown Het
Dennd5b T C 6: 148,969,806 (GRCm39) T216A probably benign Het
Dpep2 A T 8: 106,715,453 (GRCm39) M356K probably damaging Het
Dtymk A G 1: 93,722,446 (GRCm39) probably null Het
Fam91a1 A G 15: 58,287,565 (GRCm39) D4G possibly damaging Het
Fbxl20 A G 11: 97,983,955 (GRCm39) L306P probably damaging Het
Fchsd1 C T 18: 38,098,946 (GRCm39) probably benign Het
Fndc1 G A 17: 7,983,933 (GRCm39) T1331I unknown Het
Gpatch8 T C 11: 102,371,375 (GRCm39) D721G unknown Het
Gsg1 A T 6: 135,221,348 (GRCm39) I17N possibly damaging Het
Heyl A G 4: 123,140,423 (GRCm39) *327W probably null Het
Kif13b G T 14: 65,016,911 (GRCm39) R1359L probably damaging Het
Map3k14 C T 11: 103,128,380 (GRCm39) G414S probably damaging Het
Meis2 C T 2: 115,699,274 (GRCm39) A330T probably damaging Het
Mrpl9 T C 3: 94,351,003 (GRCm39) L61P probably damaging Het
Mrps6 A G 16: 91,896,548 (GRCm39) N38D probably benign Het
Muc4 C T 16: 32,575,465 (GRCm39) T1407I probably benign Het
Nup107 A G 10: 117,599,708 (GRCm39) Y604H probably damaging Het
Pgm2l1 T C 7: 99,904,826 (GRCm39) probably null Het
Pisd T C 5: 32,895,756 (GRCm39) I441V probably benign Het
Rb1cc1 T C 1: 6,308,520 (GRCm39) F52S probably damaging Het
Rnft1 T A 11: 86,386,740 (GRCm39) W383R probably damaging Het
Tas2r104 A T 6: 131,662,530 (GRCm39) W60R probably damaging Het
Tlr11 A G 14: 50,598,373 (GRCm39) T120A probably benign Het
Tmem150b T G 7: 4,726,896 (GRCm39) I71L probably benign Het
Zfp296 A G 7: 19,311,760 (GRCm39) D89G possibly damaging Het
Other mutations in Chl1
AlleleSourceChrCoordTypePredicted EffectPPH Score
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
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 2012-04-20