Incidental Mutation 'R6393:Clrn1'
ID 515850
Institutional Source Beutler Lab
Gene Symbol Clrn1
Ensembl Gene ENSMUSG00000043850
Gene Name clarin 1
Synonyms clarin-1, USH3, Ush3a, A130002D11Rik
MMRRC Submission 044542-MU
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R6393 (G1)
Quality Score 225.009
Status Validated
Chromosome 3
Chromosomal Location 58751449-58792633 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 58753741 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Phenylalanine to Leucine at position 207 (F207L)
Ref Sequence ENSEMBL: ENSMUSP00000052254 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000051408] [ENSMUST00000055636] [ENSMUST00000072551]
AlphaFold Q8K445
Predicted Effect probably damaging
Transcript: ENSMUST00000051408
AA Change: F189L

PolyPhen 2 Score 0.995 (Sensitivity: 0.68; Specificity: 0.97)
SMART Domains Protein: ENSMUSP00000051738
Gene: ENSMUSG00000043850
AA Change: F189L

DomainStartEndE-ValueType
Pfam:Claudin_2 18 208 1.8e-11 PFAM
Predicted Effect probably damaging
Transcript: ENSMUST00000055636
AA Change: F207L

PolyPhen 2 Score 0.995 (Sensitivity: 0.68; Specificity: 0.97)
SMART Domains Protein: ENSMUSP00000052254
Gene: ENSMUSG00000043850
AA Change: F207L

DomainStartEndE-ValueType
signal peptide 1 27 N/A INTRINSIC
transmembrane domain 116 138 N/A INTRINSIC
transmembrane domain 153 175 N/A INTRINSIC
transmembrane domain 207 229 N/A INTRINSIC
Predicted Effect probably damaging
Transcript: ENSMUST00000072551
AA Change: F129L

PolyPhen 2 Score 0.991 (Sensitivity: 0.71; Specificity: 0.97)
SMART Domains Protein: ENSMUSP00000072363
Gene: ENSMUSG00000043850
AA Change: F129L

DomainStartEndE-ValueType
signal peptide 1 27 N/A INTRINSIC
SCOP:d1hw7a_ 65 87 5e-3 SMART
transmembrane domain 129 151 N/A INTRINSIC
Predicted Effect noncoding transcript
Transcript: ENSMUST00000161419
Meta Mutation Damage Score 0.7530 question?
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 99.9%
  • 10x: 99.1%
  • 20x: 96.8%
Validation Efficiency 99% (70/71)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a protein that contains a cytosolic N-terminus, multiple helical transmembrane domains, and an endoplasmic reticulum membrane retention signal, TKGH, in the C-terminus. The encoded protein may be important in development and homeostasis of the inner ear and retina. Mutations within this gene have been associated with Usher syndrome type IIIa. Multiple transcript variants encoding distinct isoforms have been identified for this gene. [provided by RefSeq, Jul 2008]
PHENOTYPE: Mice homozygous for a null allele exhibit progressive hearing loss and loss of balance associated with defects in outer hair cells and supporting cells. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 71 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
A130010J15Rik A G 1: 192,856,690 (GRCm39) Q14R possibly damaging Het
Adamts12 A G 15: 11,255,721 (GRCm39) D430G probably damaging Het
Agxt2 T C 15: 10,393,894 (GRCm39) probably null Het
Akirin1 T G 4: 123,637,324 (GRCm39) Q87P possibly damaging Het
Ank2 G A 3: 126,723,406 (GRCm39) R974C probably damaging Het
Arhgap23 A G 11: 97,354,498 (GRCm39) I804V probably damaging Het
Arhgef28 A T 13: 98,130,527 (GRCm39) L437Q possibly damaging Het
Atp8a2 G T 14: 60,011,204 (GRCm39) Y967* probably null Het
Calcr A G 6: 3,708,586 (GRCm39) L200S probably damaging Het
Ccdc80 T A 16: 44,916,828 (GRCm39) V528D possibly damaging Het
Chd6 A G 2: 160,821,407 (GRCm39) Y1296H probably damaging Het
Chst13 G A 6: 90,302,063 (GRCm39) R28C possibly damaging Het
Col12a1 T C 9: 79,562,767 (GRCm39) T1772A probably damaging Het
Cubn T C 2: 13,360,491 (GRCm39) T1744A probably benign Het
Dchs2 A G 3: 83,037,218 (GRCm39) E655G probably damaging Het
Dnajb3 T A 1: 88,133,384 (GRCm39) E6V possibly damaging Het
Dock5 G A 14: 68,060,051 (GRCm39) P463S probably benign Het
Eif4a3l1 A G 6: 136,305,596 (GRCm39) K19R probably benign Het
Fancd2 T A 6: 113,555,374 (GRCm39) C1128S probably benign Het
Fcrl5 G A 3: 87,355,634 (GRCm39) G449E probably damaging Het
Frem2 G T 3: 53,493,061 (GRCm39) N1818K possibly damaging Het
Gm21149 C A 5: 15,678,037 (GRCm39) V187L possibly damaging Het
Gpat2 G C 2: 127,273,838 (GRCm39) G294R possibly damaging Het
Gstm7 A G 3: 107,838,142 (GRCm39) probably null Het
Htr1b T A 9: 81,513,810 (GRCm39) I266F probably benign Het
Jakmip3 T C 7: 138,620,900 (GRCm39) I305T probably damaging Het
Kif13a C T 13: 46,905,931 (GRCm39) V671M possibly damaging Het
Kifc5b T C 17: 27,140,816 (GRCm39) C97R probably benign Het
Klhl30 A T 1: 91,288,912 (GRCm39) H557L probably damaging Het
Lama3 T C 18: 12,612,813 (GRCm39) V1199A probably benign Het
Lmbr1 A G 5: 29,459,292 (GRCm39) L246P probably damaging Het
M6pr T C 6: 122,292,339 (GRCm39) L178P possibly damaging Het
Med17 A G 9: 15,185,879 (GRCm39) S212P probably damaging Het
Med23 T A 10: 24,749,374 (GRCm39) S31T possibly damaging Het
Morc2b T G 17: 33,356,750 (GRCm39) T341P probably damaging Het
Mre11a A G 9: 14,696,805 (GRCm39) M1V probably null Het
Mrpl17 T C 7: 105,459,122 (GRCm39) H158R probably benign Het
Mstn A G 1: 53,105,648 (GRCm39) Q330R probably benign Het
Muc16 T A 9: 18,558,695 (GRCm39) K2533* probably null Het
N4bp2 T C 5: 65,948,344 (GRCm39) S325P possibly damaging Het
Nadk A G 4: 155,673,808 (GRCm39) Y399C possibly damaging Het
Nbea A C 3: 55,998,540 (GRCm39) L89R probably damaging Het
Ncoa1 A G 12: 4,328,181 (GRCm39) F775L probably benign Het
Ndufa11 C A 17: 57,028,331 (GRCm39) A70E probably damaging Het
Nfx1 A G 4: 40,976,851 (GRCm39) Y175C possibly damaging Het
Or10q3 A T 19: 11,848,091 (GRCm39) L163Q probably damaging Het
Or12e9 A G 2: 87,201,909 (GRCm39) N11S probably damaging Het
Pcsk6 T C 7: 65,618,762 (GRCm39) S443P probably damaging Het
Pcsk9 T C 4: 106,304,793 (GRCm39) D425G probably benign Het
Pdcd1lg2 T A 19: 29,414,698 (GRCm39) C42S probably damaging Het
Peg10 GC GCTCC 6: 4,756,452 (GRCm39) probably benign Het
Rbm46 G A 3: 82,771,262 (GRCm39) T451M probably benign Het
Rcan2 T A 17: 44,264,370 (GRCm39) V10D probably benign Het
Rpl7l1 T C 17: 47,093,548 (GRCm39) E4G probably benign Het
Rptn A G 3: 93,304,506 (GRCm39) E613G probably benign Het
Sbk2 T C 7: 4,960,621 (GRCm39) D183G probably damaging Het
Slc15a4 C T 5: 127,693,950 (GRCm39) A162T probably benign Het
Slc30a4 A G 2: 122,527,966 (GRCm39) W315R probably damaging Het
Slc39a14 G C 14: 70,547,262 (GRCm39) F361L probably benign Het
Slc6a13 T C 6: 121,313,801 (GRCm39) Y515H possibly damaging Het
Slitrk3 C A 3: 72,957,247 (GRCm39) K508N possibly damaging Het
Stard4 T C 18: 33,338,278 (GRCm39) D144G probably benign Het
Tlr9 T C 9: 106,102,136 (GRCm39) F476L probably damaging Het
Tshz1 A T 18: 84,031,345 (GRCm39) V1021D probably damaging Het
Vmn1r54 A T 6: 90,246,304 (GRCm39) I73F probably benign Het
Vmn2r19 A C 6: 123,293,112 (GRCm39) S385R possibly damaging Het
Xkr5 A G 8: 18,998,716 (GRCm39) L34P probably damaging Het
Xpo4 A G 14: 57,875,770 (GRCm39) V121A probably damaging Het
Zbtb40 T A 4: 136,712,177 (GRCm39) H268L probably null Het
Zfp865 T C 7: 5,033,065 (GRCm39) F350S probably damaging Het
Zscan4b T C 7: 10,634,828 (GRCm39) I472V possibly damaging Het
Other mutations in Clrn1
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL01065:Clrn1 APN 3 58,792,446 (GRCm39) missense probably damaging 0.99
IGL03184:Clrn1 APN 3 58,753,645 (GRCm39) missense probably benign 0.00
IGL03187:Clrn1 APN 3 58,753,854 (GRCm39) missense probably damaging 0.99
R0015:Clrn1 UTSW 3 58,753,848 (GRCm39) missense probably damaging 0.99
R0015:Clrn1 UTSW 3 58,753,848 (GRCm39) missense probably damaging 0.99
R1055:Clrn1 UTSW 3 58,772,531 (GRCm39) missense probably benign 0.38
R2301:Clrn1 UTSW 3 58,753,773 (GRCm39) missense probably damaging 1.00
R4753:Clrn1 UTSW 3 58,792,318 (GRCm39) missense probably damaging 1.00
R5493:Clrn1 UTSW 3 58,753,837 (GRCm39) missense probably damaging 1.00
R5916:Clrn1 UTSW 3 58,753,783 (GRCm39) missense probably benign 0.13
R6719:Clrn1 UTSW 3 58,753,861 (GRCm39) missense probably damaging 0.99
R7722:Clrn1 UTSW 3 58,753,755 (GRCm39) missense possibly damaging 0.52
R8824:Clrn1 UTSW 3 58,792,314 (GRCm39) missense probably benign 0.12
R9342:Clrn1 UTSW 3 58,792,251 (GRCm39) missense probably benign 0.01
R9681:Clrn1 UTSW 3 58,792,251 (GRCm39) missense probably benign 0.01
Predicted Primers PCR Primer
(F):5'- TGGCCAAAGGAAGTCCATATCC -3'
(R):5'- CAAGCTCATGACTGCAGTTTTAC -3'

Sequencing Primer
(F):5'- GCCAAAGGAAGTCCATATCCTTATTG -3'
(R):5'- CCACGTAATATTTGTCCTAAGCTG -3'
Posted On 2018-05-04