Incidental Mutation 'R0015:Clrn1'
ID 8318
Institutional Source Beutler Lab
Gene Symbol Clrn1
Ensembl Gene ENSMUSG00000043850
Gene Name clarin 1
Synonyms clarin-1, USH3, Ush3a, A130002D11Rik
MMRRC Submission 038310-MU
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R0015 (G1)
Quality Score
Status Validated
Chromosome 3
Chromosomal Location 58751449-58792633 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to T at 58753848 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Isoleucine to Lysine at position 171 (I171K)
Ref Sequence ENSEMBL: ENSMUSP00000052254 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000051408] [ENSMUST00000055636] [ENSMUST00000072551]
AlphaFold Q8K445
Predicted Effect possibly damaging
Transcript: ENSMUST00000051408
AA Change: I153K

PolyPhen 2 Score 0.856 (Sensitivity: 0.83; Specificity: 0.93)
SMART Domains Protein: ENSMUSP00000051738
Gene: ENSMUSG00000043850
AA Change: I153K

DomainStartEndE-ValueType
Pfam:Claudin_2 18 208 1.8e-11 PFAM
Predicted Effect probably damaging
Transcript: ENSMUST00000055636
AA Change: I171K

PolyPhen 2 Score 0.990 (Sensitivity: 0.72; Specificity: 0.97)
SMART Domains Protein: ENSMUSP00000052254
Gene: ENSMUSG00000043850
AA Change: I171K

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 benign
Transcript: ENSMUST00000072551
AA Change: I93K

PolyPhen 2 Score 0.329 (Sensitivity: 0.90; Specificity: 0.89)
SMART Domains Protein: ENSMUSP00000072363
Gene: ENSMUSG00000043850
AA Change: I93K

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 0.1468 question?
Coding Region Coverage
  • 1x: 80.5%
  • 3x: 72.2%
  • 10x: 49.0%
  • 20x: 28.4%
Validation Efficiency 90% (88/98)
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: 46 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
A130050O07Rik A G 1: 137,856,394 (GRCm39) Y23C unknown Het
Aadat C T 8: 60,987,605 (GRCm39) probably benign Het
Adcy3 G A 12: 4,245,260 (GRCm39) probably null Het
Armc3 A G 2: 19,301,132 (GRCm39) probably null Het
Astn2 T G 4: 66,184,619 (GRCm39) probably null Het
Borcs8 T C 8: 70,593,017 (GRCm39) probably benign Het
Cacna1d G A 14: 29,836,928 (GRCm39) T804I probably benign Het
Card19 A G 13: 49,361,532 (GRCm39) L33P probably benign Het
Ccny A C 18: 9,316,682 (GRCm39) probably benign Het
Cdh5 C T 8: 104,867,559 (GRCm39) T612I probably benign Het
Cfap58 A G 19: 48,017,539 (GRCm39) M800V probably benign Het
Cnp T A 11: 100,469,734 (GRCm39) probably null Het
Col12a1 T C 9: 79,558,667 (GRCm39) T1933A probably damaging Het
Cplane1 G A 15: 8,215,668 (GRCm39) R408H probably damaging Het
Cwf19l2 A G 9: 3,454,666 (GRCm39) S660G probably benign Het
Dync1i2 C A 2: 71,044,828 (GRCm39) R13S probably damaging Het
Fat4 T A 3: 39,036,652 (GRCm39) S3435T probably damaging Het
Fchsd1 A G 18: 38,096,012 (GRCm39) C533R probably benign Het
Fstl5 G A 3: 76,229,498 (GRCm39) V100M probably damaging Het
Gria2 C T 3: 80,615,074 (GRCm39) G469S probably damaging Het
Hsf5 C A 11: 87,548,161 (GRCm39) H615N probably benign Het
Ints2 T C 11: 86,140,113 (GRCm39) T240A probably damaging Het
Kcnn3 A C 3: 89,570,080 (GRCm39) D631A probably damaging Het
Lama4 C T 10: 38,951,432 (GRCm39) T1059M possibly damaging Het
Lgals8 A G 13: 12,462,179 (GRCm39) L226P probably damaging Het
Lonp1 T A 17: 56,925,406 (GRCm39) Q462L probably benign Het
Mark2 A T 19: 7,263,142 (GRCm39) Y231* probably null Het
Mdh1b T C 1: 63,760,959 (GRCm39) probably benign Het
Myh7b C T 2: 155,464,206 (GRCm39) P569L probably damaging Het
Myl3 A C 9: 110,596,997 (GRCm39) D119A probably damaging Het
Ncapd3 C A 9: 26,963,105 (GRCm39) A470E probably damaging Het
Ndrg2 A G 14: 52,147,902 (GRCm39) probably benign Het
Nprl2 A T 9: 107,421,618 (GRCm39) I209F probably damaging Het
Pcf11 T A 7: 92,307,525 (GRCm39) H881L probably benign Het
Pde10a A G 17: 9,196,029 (GRCm39) D640G probably damaging Het
Pdxdc1 A T 16: 13,705,547 (GRCm39) probably benign Het
Polr2g A G 19: 8,771,016 (GRCm39) I160T probably damaging Het
Pter G A 2: 13,005,811 (GRCm39) G328D probably damaging Het
Rad51 T A 2: 118,946,808 (GRCm39) M5K probably benign Het
Rbm43 T A 2: 51,815,679 (GRCm39) I181F probably benign Het
Rgs12 T C 5: 35,180,120 (GRCm39) probably benign Het
Slc20a2 C A 8: 23,025,361 (GRCm39) A21E probably damaging Het
Sybu T C 15: 44,536,896 (GRCm39) R349G probably damaging Het
Tmem161b C A 13: 84,370,533 (GRCm39) probably null Het
Xirp2 C A 2: 67,341,243 (GRCm39) Y1161* probably null Het
Zfand4 C A 6: 116,305,258 (GRCm39) T705K probably 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
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
R6393:Clrn1 UTSW 3 58,753,741 (GRCm39) missense probably damaging 1.00
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
Posted On 2012-11-21