Incidental Mutation 'R8059:Chl1'
ID 619594
Institutional Source Beutler Lab
Gene Symbol Chl1
Ensembl Gene ENSMUSG00000030077
Gene Name cell adhesion molecule L1-like
Synonyms A530023M13Rik, close homolog of L1, LICAM2, CALL
MMRRC Submission 067894-MU
Accession Numbers
Essential gene? Possibly essential (E-score: 0.524) question?
Stock # R8059 (G1)
Quality Score 225.009
Status Validated
Chromosome 6
Chromosomal Location 103487372-103709999 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to A at 103651948 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Isoleucine to Asparagine at position 272 (I272N)
Ref Sequence ENSEMBL: ENSMUSP00000063933 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000066905] [ENSMUST00000203830] [ENSMUST00000203912]
AlphaFold P70232
Predicted Effect probably damaging
Transcript: ENSMUST00000066905
AA Change: I272N

PolyPhen 2 Score 0.968 (Sensitivity: 0.77; Specificity: 0.95)
SMART Domains Protein: ENSMUSP00000063933
Gene: ENSMUSG00000030077
AA Change: I272N

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 damaging
Transcript: ENSMUST00000203830
AA Change: I272N

PolyPhen 2 Score 0.968 (Sensitivity: 0.77; Specificity: 0.95)
SMART Domains Protein: ENSMUSP00000144758
Gene: ENSMUSG00000030077
AA Change: I272N

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 damaging
Transcript: ENSMUST00000203912
AA Change: I288N

PolyPhen 2 Score 0.988 (Sensitivity: 0.73; Specificity: 0.96)
SMART Domains Protein: ENSMUSP00000145026
Gene: ENSMUSG00000030077
AA Change: I288N

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
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 100.0%
  • 10x: 99.7%
  • 20x: 99.1%
Validation Efficiency 100% (58/58)
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: 57 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abca13 T A 11: 9,323,279 (GRCm39) M3372K probably benign Het
Abcg3 A T 5: 105,100,948 (GRCm39) probably null Het
Adam19 G A 11: 46,027,293 (GRCm39) probably benign Het
Adgrg6 G T 10: 14,344,794 (GRCm39) T53K probably damaging Het
Ccdc141 A C 2: 76,875,095 (GRCm39) L705R probably damaging Het
Cep78 A T 19: 15,958,876 (GRCm39) V156E probably benign Het
Cers2 A G 3: 95,229,982 (GRCm39) D342G probably damaging Het
Defb30 A G 14: 63,273,383 (GRCm39) *77Q probably null Het
Dnai3 C G 3: 145,752,428 (GRCm39) R749S possibly damaging Het
Dnm3 A G 1: 161,911,708 (GRCm39) V63A probably damaging Het
Dsc2 C T 18: 20,165,331 (GRCm39) G881R possibly damaging Het
Entpd2 G T 2: 25,288,096 (GRCm39) V107L probably damaging Het
Hectd1 T A 12: 51,837,161 (GRCm39) H799L possibly damaging Het
Hira T C 16: 18,730,901 (GRCm39) V200A probably damaging Het
Hspd1 T C 1: 55,120,883 (GRCm39) K269E possibly damaging Het
Kcnj4 T C 15: 79,369,003 (GRCm39) S326G probably benign Het
Kctd19 T G 8: 106,122,983 (GRCm39) I144L probably benign Het
Lama4 T C 10: 38,842,057 (GRCm39) I36T probably benign Het
Lrrn3 T C 12: 41,504,216 (GRCm39) T34A probably benign Het
Maco1 A T 4: 134,555,359 (GRCm39) C371* probably null Het
Maml3 A G 3: 51,764,110 (GRCm39) S285P probably damaging Het
Man2b2 A G 5: 36,973,504 (GRCm39) Y492H probably damaging Het
Mapk10 G T 5: 103,114,478 (GRCm39) N303K probably damaging Het
Matn2 C T 15: 34,345,481 (GRCm39) R163C probably damaging Het
Mtmr7 C T 8: 41,034,564 (GRCm39) A253T probably damaging Het
Naca C T 10: 127,876,372 (GRCm39) P468L unknown Het
Nckap1l T C 15: 103,401,714 (GRCm39) S1084P possibly damaging Het
Nek11 T C 9: 105,040,173 (GRCm39) *629W probably null Het
Nfkb1 C T 3: 135,299,613 (GRCm39) A731T possibly damaging Het
Nop2 T C 6: 125,117,775 (GRCm39) V442A probably damaging Het
Oaz2 C T 9: 65,596,425 (GRCm39) P163L probably damaging Het
Or5p57 T C 7: 107,665,223 (GRCm39) T231A probably benign Het
Or6d14 C T 6: 116,533,434 (GRCm39) T16I possibly damaging Het
Or8k23 A G 2: 86,186,306 (GRCm39) V140A probably benign Het
Pabpc2 A T 18: 39,907,875 (GRCm39) N380I probably benign Het
Pax3 T C 1: 78,080,003 (GRCm39) D461G probably benign Het
Pds5b G T 5: 150,731,300 (GRCm39) R1443L unknown Het
Per1 G A 11: 68,997,309 (GRCm39) R828H probably damaging Het
Phlpp2 T A 8: 110,622,189 (GRCm39) S144T probably benign Het
Plod1 A T 4: 148,012,941 (GRCm39) I207N probably damaging Het
Psmc6 A T 14: 45,578,260 (GRCm39) I208F probably damaging Het
Rev3l T C 10: 39,719,491 (GRCm39) S2494P probably damaging Het
Rgs3 T C 4: 62,521,214 (GRCm39) probably benign Het
Rtraf T C 14: 19,872,631 (GRCm39) probably benign Het
Slc17a6 T A 7: 51,294,792 (GRCm39) N166K probably damaging Het
Slc18a2 A T 19: 59,272,572 (GRCm39) T348S probably benign Het
Slc39a8 G T 3: 135,532,347 (GRCm39) A39S probably benign Het
Slc8a3 C T 12: 81,249,032 (GRCm39) G799S probably damaging Het
Sp1 T G 15: 102,316,337 (GRCm39) S46R possibly damaging Het
Spta1 A G 1: 174,045,936 (GRCm39) probably benign Het
Stab1 G A 14: 30,882,198 (GRCm39) P499L probably benign Het
Trav21-dv12 C A 14: 54,114,178 (GRCm39) D99E probably damaging Het
Trpv6 T G 6: 41,601,520 (GRCm39) I467L probably benign Het
Ttc41 A G 10: 86,548,842 (GRCm39) Y12C probably benign Het
Vmn1r233 T C 17: 21,214,698 (GRCm39) N84S probably benign Het
Vrtn T C 12: 84,696,690 (GRCm39) F480S probably benign Het
Zc3h13 C G 14: 75,565,250 (GRCm39) R788G unknown Het
Other mutations in Chl1
AlleleSourceChrCoordTypePredicted EffectPPH 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
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
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
Predicted Primers PCR Primer
(F):5'- GTAGACTTAGCCTCCTTCCAGAAC -3'
(R):5'- CGTACCTTCTACTGTGACGTG -3'

Sequencing Primer
(F):5'- TTCCTAGGGAGTAGACCATTAAAAG -3'
(R):5'- GTGAAAATCATGACTGGCTTTCCC -3'
Posted On 2020-01-23