Incidental Mutation 'R5916:Clrn1'
ID 461314
Institutional Source Beutler Lab
Gene Symbol Clrn1
Ensembl Gene ENSMUSG00000043850
Gene Name clarin 1
Synonyms clarin-1, USH3, Ush3a, A130002D11Rik
MMRRC Submission 044113-MU
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R5916 (G1)
Quality Score 225
Status Not validated
Chromosome 3
Chromosomal Location 58751449-58792633 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 58753783 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Threonine to Alanine at position 193 (T193A)
Ref Sequence ENSEMBL: ENSMUSP00000052254 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000051408] [ENSMUST00000055636] [ENSMUST00000072551]
AlphaFold Q8K445
Predicted Effect probably benign
Transcript: ENSMUST00000051408
AA Change: T175A

PolyPhen 2 Score 0.031 (Sensitivity: 0.95; Specificity: 0.82)
SMART Domains Protein: ENSMUSP00000051738
Gene: ENSMUSG00000043850
AA Change: T175A

DomainStartEndE-ValueType
Pfam:Claudin_2 18 208 1.8e-11 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000055636
AA Change: T193A

PolyPhen 2 Score 0.126 (Sensitivity: 0.93; Specificity: 0.86)
SMART Domains Protein: ENSMUSP00000052254
Gene: ENSMUSG00000043850
AA Change: T193A

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: T115A

PolyPhen 2 Score 0.007 (Sensitivity: 0.96; Specificity: 0.75)
SMART Domains Protein: ENSMUSP00000072363
Gene: ENSMUSG00000043850
AA Change: T115A

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
Coding Region Coverage
  • 1x: 99.8%
  • 3x: 99.3%
  • 10x: 97.2%
  • 20x: 92.4%
Validation Efficiency
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: 61 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Aadacl4 A T 4: 144,349,550 (GRCm39) N269I possibly damaging Het
Abcc1 G T 16: 14,283,006 (GRCm39) V1161F possibly damaging Het
Adam3 A T 8: 25,174,555 (GRCm39) probably null Het
Agt A T 8: 125,290,597 (GRCm39) S237T possibly damaging Het
Ano3 A T 2: 110,512,181 (GRCm39) F674L probably benign Het
Asb2 G T 12: 103,290,135 (GRCm39) A504E probably damaging Het
Atp13a1 T A 8: 70,259,748 (GRCm39) I1113N probably damaging Het
Atxn7l2 T C 3: 108,112,978 (GRCm39) probably null Het
Bambi A G 18: 3,511,463 (GRCm39) T95A probably benign Het
Cfap210 A T 2: 69,619,806 (GRCm39) M1K probably null Het
Colgalt2 T A 1: 152,379,873 (GRCm39) D437E probably damaging Het
Dchs1 C A 7: 105,408,373 (GRCm39) A1820S probably damaging Het
Dnah12 T A 14: 26,428,073 (GRCm39) I233N possibly damaging Het
Dsc3 T C 18: 20,120,077 (GRCm39) N194D probably damaging Het
Dync2h1 A G 9: 7,102,309 (GRCm39) probably null Het
Erich3 A T 3: 154,401,460 (GRCm39) R36S probably damaging Het
Fam243 T A 16: 92,117,559 (GRCm39) E243V probably damaging Het
Fmnl3 A T 15: 99,219,709 (GRCm39) C680S probably damaging Het
Focad T C 4: 88,275,778 (GRCm39) L1129P unknown Het
Fzd3 G A 14: 65,440,178 (GRCm39) T664I probably benign Het
Glb1l3 T C 9: 26,766,032 (GRCm39) I129V probably benign Het
Heatr1 T C 13: 12,449,352 (GRCm39) F1950S probably damaging Het
Herc6 G A 6: 57,623,188 (GRCm39) G597E probably benign Het
Hmcn2 T A 2: 31,286,151 (GRCm39) V2101D probably damaging Het
Il17re T A 6: 113,447,084 (GRCm39) C612S probably damaging Het
Il36g T G 2: 24,082,806 (GRCm39) *194E probably null Het
Junb T C 8: 85,704,505 (GRCm39) Y185C probably benign Het
Lrriq1 G A 10: 103,057,243 (GRCm39) Q186* probably null Het
Lrrn2 T A 1: 132,865,538 (GRCm39) V201E probably damaging Het
Ly6l A T 15: 75,323,027 (GRCm39) T68S probably benign Het
Marchf1 G T 8: 66,839,763 (GRCm39) R182L possibly damaging Het
Megf6 A G 4: 154,333,882 (GRCm39) probably null Het
Mga T A 2: 119,794,793 (GRCm39) S2708T probably benign Het
Mx1 T C 16: 97,252,933 (GRCm39) T396A probably benign Het
Naip5 A C 13: 100,359,209 (GRCm39) S676A probably benign Het
Npepl1 G T 2: 173,963,337 (GRCm39) W456C probably benign Het
Ntrk2 A G 13: 58,956,543 (GRCm39) M1V probably null Het
Nufip1 T C 14: 76,372,340 (GRCm39) *485Q probably null Het
Ocln T G 13: 100,642,687 (GRCm39) D216A possibly damaging Het
Or10x1 A T 1: 174,196,698 (GRCm39) T72S probably damaging Het
Or1o11 C T 17: 37,756,570 (GRCm39) L53F probably benign Het
Or4f57 A G 2: 111,791,175 (GRCm39) M81T probably damaging Het
Or55b4 G A 7: 102,133,586 (GRCm39) S247F probably damaging Het
Ptprq A T 10: 107,359,374 (GRCm39) M2243K probably damaging Het
Rad51b C T 12: 79,371,856 (GRCm39) Q190* probably null Het
Resf1 C T 6: 149,228,076 (GRCm39) T374I probably damaging Het
Rfx8 T C 1: 39,727,779 (GRCm39) Y182C probably benign Het
Rpgrip1l C A 8: 91,979,541 (GRCm39) R967L possibly damaging Het
Scube2 A G 7: 109,430,931 (GRCm39) Y423H possibly damaging Het
Sipa1l2 A T 8: 126,195,312 (GRCm39) Y809N probably damaging Het
Slc35f1 C A 10: 52,809,317 (GRCm39) Y101* probably null Het
Tbc1d22a A G 15: 86,098,809 (GRCm39) K12E possibly damaging Het
Tent2 T C 13: 93,312,055 (GRCm39) D215G probably damaging Het
Tmcc2 C T 1: 132,285,429 (GRCm39) V646M probably damaging Het
Tpp1 A T 7: 105,398,587 (GRCm39) M243K probably damaging Het
Trappc12 A G 12: 28,741,513 (GRCm39) L732P probably damaging Het
U2af2 A T 7: 5,082,179 (GRCm39) probably null Het
Utrn T A 10: 12,540,795 (GRCm39) N1877Y probably damaging Het
Vsir C T 10: 60,193,816 (GRCm39) T93I probably damaging Het
Zkscan5 T A 5: 145,142,112 (GRCm39) M3K possibly damaging Het
Zscan29 G T 2: 120,994,518 (GRCm39) T489N 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
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
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
Predicted Primers PCR Primer
(F):5'- TGGCCAAAGGAAGTCCATATCC -3'
(R):5'- GAATCAAGCTCATGACTGCAG -3'

Sequencing Primer
(F):5'- GCCAAAGGAAGTCCATATCCTTATTG -3'
(R):5'- CAAGCTCATGACTGCAGTTTTAC -3'
Posted On 2017-02-28