Incidental Mutation 'R5986:Chl1'
ID 481647
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 044166-MU
Accession Numbers
Essential gene? Possibly non essential (E-score: 0.458) question?
Stock # R5986 (G1)
Quality Score 225.009
Status Not validated
Chromosome 6
Chromosomal Location 103487372-103709999 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) C to A at 103686152 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Leucine to Isoleucine at position 954 (L954I)
Ref Sequence ENSEMBL: ENSMUSP00000145026 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000066905] [ENSMUST00000203830] [ENSMUST00000203912] [ENSMUST00000205098]
AlphaFold P70232
Predicted Effect probably benign
Transcript: ENSMUST00000066905
AA Change: L938I

PolyPhen 2 Score 0.041 (Sensitivity: 0.94; Specificity: 0.83)
SMART Domains Protein: ENSMUSP00000063933
Gene: ENSMUSG00000030077
AA Change: L938I

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: L938I

PolyPhen 2 Score 0.041 (Sensitivity: 0.94; Specificity: 0.83)
SMART Domains Protein: ENSMUSP00000144758
Gene: ENSMUSG00000030077
AA Change: L938I

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: L954I

PolyPhen 2 Score 0.450 (Sensitivity: 0.89; Specificity: 0.90)
SMART Domains Protein: ENSMUSP00000145026
Gene: ENSMUSG00000030077
AA Change: L954I

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
AA Change: L211I

PolyPhen 2 Score 0.006 (Sensitivity: 0.97; Specificity: 0.75)
SMART Domains Protein: ENSMUSP00000144739
Gene: ENSMUSG00000030077
AA Change: L211I

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
  • 1x: 99.9%
  • 3x: 99.5%
  • 10x: 97.7%
  • 20x: 92.7%
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: 56 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Agl A T 3: 116,566,145 (GRCm39) F992I probably damaging Het
Ampd1 T C 3: 102,992,713 (GRCm39) F152L probably damaging Het
Ank2 T C 3: 126,806,335 (GRCm39) H602R possibly damaging Het
Ankib1 T C 5: 3,797,071 (GRCm39) D247G probably damaging Het
Bccip T A 7: 133,322,594 (GRCm39) H313Q probably benign Het
Ccdc198 A T 14: 49,470,403 (GRCm39) L172H probably damaging Het
Cep250 A G 2: 155,821,197 (GRCm39) E929G probably damaging Het
Cog5 A T 12: 31,710,716 (GRCm39) D32V probably benign Het
Cyp4f16 C A 17: 32,763,116 (GRCm39) A187E probably benign Het
Dffb A T 4: 154,050,050 (GRCm39) V271E probably damaging Het
Dnah8 A G 17: 31,070,604 (GRCm39) Y4430C possibly damaging Het
Dpp3 T C 19: 4,968,385 (GRCm39) E229G probably benign Het
Fat3 T A 9: 15,909,613 (GRCm39) N2130Y probably benign Het
Kcnk3 T C 5: 30,745,722 (GRCm39) V21A possibly damaging Het
Kif9 G A 9: 110,319,094 (GRCm39) S186N probably benign Het
Lhfpl3 C A 5: 22,951,424 (GRCm39) N78K probably benign Het
Ly6c1 A G 15: 74,917,457 (GRCm39) S64P probably damaging Het
Mapk10 T C 5: 103,186,446 (GRCm39) T59A probably benign Het
Mars1 A T 10: 127,140,171 (GRCm39) C394* probably null Het
Mettl16 T A 11: 74,683,063 (GRCm39) D168E possibly damaging Het
Mgat2 A T 12: 69,232,158 (GRCm39) Q244L probably benign Het
Mrps30 A G 13: 118,521,101 (GRCm39) probably null Het
Myrip C A 9: 120,290,487 (GRCm39) A702E probably damaging Het
Nepn T C 10: 52,280,168 (GRCm39) L420P probably damaging Het
Nrn1 A T 13: 36,918,238 (GRCm39) Y9* probably null Het
Nup107 T C 10: 117,595,081 (GRCm39) Y752C probably damaging Het
Nutm2 A T 13: 50,628,496 (GRCm39) D520V probably damaging Het
Olfm2 C T 9: 20,586,946 (GRCm39) C48Y probably damaging Het
Or52j3 T C 7: 102,836,735 (GRCm39) F309S possibly damaging Het
Or8g19 A G 9: 39,056,278 (GRCm39) N294S probably null Het
Osbpl1a T A 18: 13,038,138 (GRCm39) D271V probably damaging Het
Osmr G T 15: 6,873,934 (GRCm39) D154E probably benign Het
Pcdh9 A G 14: 94,124,484 (GRCm39) V562A probably damaging Het
Peak1 A C 9: 56,166,726 (GRCm39) S401A probably benign Het
Pigk A T 3: 152,446,486 (GRCm39) H195L probably benign Het
Plekha6 G C 1: 133,200,045 (GRCm39) R208P possibly damaging Het
Ppp2r1a C T 17: 21,171,608 (GRCm39) R28C probably damaging Het
Pramel30 G T 4: 144,059,323 (GRCm39) V345F probably damaging Het
Ptbp3 T C 4: 59,493,311 (GRCm39) D123G probably benign Het
Ptgr2 G A 12: 84,355,120 (GRCm39) E285K possibly damaging Het
Rassf1 G T 9: 107,429,021 (GRCm39) V76L possibly damaging Het
Sec22a A G 16: 35,134,461 (GRCm39) V307A probably damaging Het
Skint5 C T 4: 113,852,845 (GRCm39) V18I probably benign Het
Slc1a5 T C 7: 16,516,151 (GRCm39) V109A probably benign Het
St8sia5 T A 18: 77,342,478 (GRCm39) M396K possibly damaging Het
Tiam1 T C 16: 89,586,074 (GRCm39) E602G probably benign Het
Tll1 T C 8: 64,527,297 (GRCm39) E408G probably damaging Het
Tpsb2 G A 17: 25,586,108 (GRCm39) V109M probably benign Het
Trib1 T A 15: 59,526,451 (GRCm39) probably null Het
Trio G T 15: 27,852,019 (GRCm39) A765E possibly damaging Het
Uggt2 A T 14: 119,286,838 (GRCm39) V193E probably damaging Het
Vmn1r115 G A 7: 20,578,447 (GRCm39) P155L probably benign Het
Wdr31 A G 4: 62,374,113 (GRCm39) L292S probably benign Het
Xrra1 T C 7: 99,525,462 (GRCm39) I127T probably benign Het
Yju2 G A 17: 56,269,030 (GRCm39) C46Y probably damaging Het
Zfp442 G A 2: 150,249,944 (GRCm39) Q596* probably null 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
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
Predicted Primers PCR Primer
(F):5'- AGCTGCCACTTATGCAAATTAC -3'
(R):5'- AGGCACATTACTGATCCCTGTG -3'

Sequencing Primer
(F):5'- CTCATAGGAGTTTACATCTGAGTTTC -3'
(R):5'- ATCCCTGTGCTATAAGGAATAGTGG -3'
Posted On 2017-06-26