Incidental Mutation 'R1855:Clptm1'
ID 206025
Institutional Source Beutler Lab
Gene Symbol Clptm1
Ensembl Gene ENSMUSG00000002981
Gene Name cleft lip and palate associated transmembrane protein 1
Synonyms N14, HS9
MMRRC Submission 039879-MU
Accession Numbers
Essential gene? Probably essential (E-score: 0.926) question?
Stock # R1855 (G1)
Quality Score 169
Status Validated
Chromosome 7
Chromosomal Location 19365505-19398955 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 19372134 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Valine to Alanine at position 234 (V234A)
Ref Sequence ENSEMBL: ENSMUSP00000051293 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000055242]
AlphaFold Q8VBZ3
Predicted Effect probably benign
Transcript: ENSMUST00000055242
AA Change: V234A

PolyPhen 2 Score 0.048 (Sensitivity: 0.94; Specificity: 0.83)
SMART Domains Protein: ENSMUSP00000051293
Gene: ENSMUSG00000002981
AA Change: V234A

DomainStartEndE-ValueType
low complexity region 2 23 N/A INTRINSIC
low complexity region 35 52 N/A INTRINSIC
Pfam:CLPTM1 56 497 5.8e-148 PFAM
transmembrane domain 507 529 N/A INTRINSIC
low complexity region 606 628 N/A INTRINSIC
low complexity region 649 664 N/A INTRINSIC
Predicted Effect noncoding transcript
Transcript: ENSMUST00000207704
Predicted Effect noncoding transcript
Transcript: ENSMUST00000208554
Predicted Effect noncoding transcript
Transcript: ENSMUST00000208846
Predicted Effect noncoding transcript
Transcript: ENSMUST00000208868
Meta Mutation Damage Score 0.1641 question?
Coding Region Coverage
  • 1x: 97.4%
  • 3x: 96.9%
  • 10x: 95.3%
  • 20x: 92.4%
Validation Efficiency 97% (72/74)
Allele List at MGI
Other mutations in this stock
Total: 71 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
A830018L16Rik T A 1: 11,818,195 (GRCm39) L285Q probably damaging Het
Acaca T C 11: 84,262,380 (GRCm39) L1994P probably damaging Het
Adamts9 A G 6: 92,878,350 (GRCm39) probably benign Het
Aff3 T C 1: 38,249,385 (GRCm39) E574G probably benign Het
Ankrd1 T C 19: 36,096,635 (GRCm39) K64R probably damaging Het
Arhgap23 T C 11: 97,339,523 (GRCm39) I163T probably damaging Het
Ascc3 A T 10: 50,494,018 (GRCm39) Q151L probably benign Het
Atad2 G A 15: 57,960,685 (GRCm39) P971L possibly damaging Het
C1s1 A C 6: 124,511,315 (GRCm39) probably null Het
Ccdc150 T C 1: 54,407,069 (GRCm39) probably benign Het
Cdhr3 A T 12: 33,110,351 (GRCm39) I311N probably damaging Het
Chad T A 11: 94,456,303 (GRCm39) L127H probably damaging Het
Clasp1 G A 1: 118,436,624 (GRCm39) A303T probably damaging Het
Cnih3 C A 1: 181,282,186 (GRCm39) S140* probably null Het
Col24a1 G A 3: 145,164,895 (GRCm39) G1033D probably damaging Het
Csnk1a1 T A 18: 61,708,498 (GRCm39) probably null Het
Cttnbp2 T A 6: 18,378,412 (GRCm39) I1475L probably benign Het
Dnah5 T C 15: 28,411,815 (GRCm39) V3728A possibly damaging Het
Dock9 C A 14: 121,877,571 (GRCm39) V391F probably damaging Het
Ehmt2 A T 17: 35,129,752 (GRCm39) I949F probably damaging Het
Eif4g1 C A 16: 20,505,911 (GRCm39) T1025K possibly damaging Het
Enpp2 C T 15: 54,709,219 (GRCm39) E803K probably damaging Het
Esrrg A T 1: 187,943,295 (GRCm39) M423L probably damaging Het
Etnppl A T 3: 130,414,371 (GRCm39) I89F probably benign Het
Fabp3 C T 4: 130,206,180 (GRCm39) T57I probably benign Het
Fbln7 A G 2: 128,735,755 (GRCm39) T248A possibly damaging Het
Galnt9 C T 5: 110,763,390 (GRCm39) T465M probably damaging Het
Grcc10 A G 6: 124,717,541 (GRCm39) V57A probably benign Het
Herc1 T A 9: 66,298,708 (GRCm39) M614K possibly damaging Het
Itch C T 2: 155,014,374 (GRCm39) probably benign Het
Kdm6b C A 11: 69,298,112 (GRCm39) A167S probably damaging Het
Kidins220 C T 12: 25,106,590 (GRCm39) R1348C probably damaging Het
Kif17 T C 4: 138,015,582 (GRCm39) L577P probably benign Het
Krt25 A T 11: 99,209,141 (GRCm39) L258Q probably damaging Het
Marchf10 T C 11: 105,281,218 (GRCm39) T356A probably benign Het
Mical2 G A 7: 111,944,489 (GRCm39) A940T probably benign Het
Mrpl4 A G 9: 20,914,667 (GRCm39) E81G possibly damaging Het
Mtcl1 A G 17: 66,686,509 (GRCm39) V447A probably benign Het
Mtor C A 4: 148,637,546 (GRCm39) N2502K probably benign Het
Notch4 G A 17: 34,799,936 (GRCm39) D966N probably benign Het
Oip5 C A 2: 119,442,271 (GRCm39) K214N probably benign Het
Or8a1b A T 9: 37,623,266 (GRCm39) F103Y possibly damaging Het
Pabir2 T A X: 52,342,933 (GRCm39) Q201H probably benign Het
Pak5 A T 2: 135,929,429 (GRCm39) S585T probably benign Het
Pard3 T A 8: 128,174,293 (GRCm39) probably null Het
Pcnx2 A T 8: 126,534,735 (GRCm39) probably benign Het
Pcsk5 T C 19: 17,492,556 (GRCm39) Y939C possibly damaging Het
Pde1a A G 2: 79,728,408 (GRCm39) probably null Het
Pde9a C T 17: 31,674,094 (GRCm39) P60S probably damaging Het
Pikfyve C A 1: 65,297,957 (GRCm39) T1562K probably benign Het
Plekhg6 A T 6: 125,352,802 (GRCm39) M115K probably damaging Het
Pogz C T 3: 94,786,160 (GRCm39) T863I probably benign Het
Ppp1r3a A T 6: 14,754,993 (GRCm39) W85R probably damaging Het
Rnf123 C A 9: 107,938,990 (GRCm39) R826L probably damaging Het
Slc1a6 T A 10: 78,648,758 (GRCm39) V493E probably damaging Het
Slc22a2 A G 17: 12,805,699 (GRCm39) D150G probably damaging Het
Snap47 C T 11: 59,319,159 (GRCm39) probably benign Het
Spata22 A G 11: 73,231,385 (GRCm39) D213G probably benign Het
St6galnac2 T A 11: 116,581,141 (GRCm39) R60S probably benign Het
Stk32c A G 7: 138,701,363 (GRCm39) F263S probably damaging Het
Supt6 T C 11: 78,123,366 (GRCm39) I104V possibly damaging Het
Tex2 T C 11: 106,437,702 (GRCm39) E158G possibly damaging Het
Tiam2 C T 17: 3,465,410 (GRCm39) R380C probably damaging Het
Trim25 C T 11: 88,906,407 (GRCm39) T410I probably benign Het
Usp18 T A 6: 121,239,076 (GRCm39) C212S probably benign Het
Vmn1r2 A G 4: 3,172,588 (GRCm39) Y169C probably damaging Het
Wdr33 A T 18: 32,039,909 (GRCm39) probably benign Het
Xpr1 A G 1: 155,159,002 (GRCm39) Y597H probably benign Het
Yy1 CGGG CGGGGGGGGG 12: 108,759,916 (GRCm39) probably benign Het
Zfp54 T A 17: 21,654,404 (GRCm39) Y299* probably null Het
Zfp566 T G 7: 29,777,927 (GRCm39) S85R probably benign Het
Other mutations in Clptm1
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL01614:Clptm1 APN 7 19,371,625 (GRCm39) missense probably benign 0.14
IGL01909:Clptm1 APN 7 19,389,701 (GRCm39) missense probably benign 0.37
IGL03089:Clptm1 APN 7 19,371,072 (GRCm39) missense probably damaging 1.00
H8786:Clptm1 UTSW 7 19,369,629 (GRCm39) missense possibly damaging 0.54
R0128:Clptm1 UTSW 7 19,368,932 (GRCm39) missense probably damaging 1.00
R0835:Clptm1 UTSW 7 19,369,599 (GRCm39) missense possibly damaging 0.61
R1167:Clptm1 UTSW 7 19,368,136 (GRCm39) missense probably damaging 1.00
R1370:Clptm1 UTSW 7 19,367,797 (GRCm39) missense possibly damaging 0.61
R1655:Clptm1 UTSW 7 19,379,792 (GRCm39) missense probably benign 0.00
R2004:Clptm1 UTSW 7 19,380,762 (GRCm39) missense possibly damaging 0.46
R2189:Clptm1 UTSW 7 19,371,070 (GRCm39) nonsense probably null
R2203:Clptm1 UTSW 7 19,367,817 (GRCm39) missense possibly damaging 0.92
R3237:Clptm1 UTSW 7 19,369,271 (GRCm39) missense probably damaging 0.99
R3963:Clptm1 UTSW 7 19,372,121 (GRCm39) nonsense probably null
R5416:Clptm1 UTSW 7 19,367,741 (GRCm39) unclassified probably benign
R6110:Clptm1 UTSW 7 19,367,731 (GRCm39) unclassified probably benign
R6474:Clptm1 UTSW 7 19,369,762 (GRCm39) missense possibly damaging 0.94
R6737:Clptm1 UTSW 7 19,371,001 (GRCm39) critical splice donor site probably null
R6897:Clptm1 UTSW 7 19,369,751 (GRCm39) missense possibly damaging 0.94
R8144:Clptm1 UTSW 7 19,367,827 (GRCm39) missense possibly damaging 0.88
R8244:Clptm1 UTSW 7 19,372,916 (GRCm39) missense possibly damaging 0.46
R8374:Clptm1 UTSW 7 19,372,081 (GRCm39) missense probably benign 0.13
R8438:Clptm1 UTSW 7 19,379,776 (GRCm39) missense probably benign 0.00
R8885:Clptm1 UTSW 7 19,372,932 (GRCm39) missense probably damaging 1.00
R9399:Clptm1 UTSW 7 19,367,842 (GRCm39) missense probably damaging 1.00
R9467:Clptm1 UTSW 7 19,371,449 (GRCm39) missense probably benign 0.04
R9529:Clptm1 UTSW 7 19,371,600 (GRCm39) missense probably benign 0.17
R9601:Clptm1 UTSW 7 19,369,763 (GRCm39) missense probably damaging 1.00
Z1177:Clptm1 UTSW 7 19,371,393 (GRCm39) critical splice donor site probably null
Predicted Primers PCR Primer
(F):5'- GTGGAACTAAAAGGGTCTCTCAC -3'
(R):5'- TGGTCCTGTGCATGAGTAGC -3'

Sequencing Primer
(F):5'- ACTAAAAGGGTCTCTCACAGATG -3'
(R):5'- AAGCCTCTCCTTGTTTCAGATGAGG -3'
Posted On 2014-06-23