Incidental Mutation 'R6345:Specc1l'
ID 514112
Institutional Source Beutler Lab
Gene Symbol Specc1l
Ensembl Gene ENSMUSG00000033444
Gene Name sperm antigen with calponin homology and coiled-coil domains 1-like
Synonyms 9530057A13Rik, Specc1l, 4932439K10Rik, 4930470P14Rik, Cytsa
MMRRC Submission 044499-MU
Accession Numbers
Essential gene? Possibly essential (E-score: 0.560) question?
Stock # R6345 (G1)
Quality Score 225.009
Status Validated
Chromosome 10
Chromosomal Location 75047872-75148234 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) G to T at 75084322 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Aspartic acid to Tyrosine at position 682 (D682Y)
Ref Sequence ENSEMBL: ENSMUSP00000101061 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000040105] [ENSMUST00000105421] [ENSMUST00000218766] [ENSMUST00000219387]
AlphaFold Q2KN98
Predicted Effect probably damaging
Transcript: ENSMUST00000040105
AA Change: D682Y

PolyPhen 2 Score 0.991 (Sensitivity: 0.71; Specificity: 0.97)
SMART Domains Protein: ENSMUSP00000045099
Gene: ENSMUSG00000033444
AA Change: D682Y

DomainStartEndE-ValueType
low complexity region 97 107 N/A INTRINSIC
low complexity region 135 149 N/A INTRINSIC
coiled coil region 255 298 N/A INTRINSIC
low complexity region 376 390 N/A INTRINSIC
coiled coil region 412 467 N/A INTRINSIC
coiled coil region 505 825 N/A INTRINSIC
low complexity region 846 858 N/A INTRINSIC
low complexity region 989 1010 N/A INTRINSIC
CH 1031 1129 1.52e-15 SMART
Predicted Effect probably damaging
Transcript: ENSMUST00000105421
AA Change: D682Y

PolyPhen 2 Score 0.991 (Sensitivity: 0.71; Specificity: 0.97)
SMART Domains Protein: ENSMUSP00000101061
Gene: ENSMUSG00000033444
AA Change: D682Y

DomainStartEndE-ValueType
low complexity region 80 90 N/A INTRINSIC
low complexity region 118 132 N/A INTRINSIC
coiled coil region 238 281 N/A INTRINSIC
low complexity region 359 373 N/A INTRINSIC
coiled coil region 395 450 N/A INTRINSIC
coiled coil region 488 808 N/A INTRINSIC
low complexity region 829 841 N/A INTRINSIC
low complexity region 972 993 N/A INTRINSIC
CH 1014 1112 1.52e-15 SMART
Predicted Effect probably damaging
Transcript: ENSMUST00000218766
AA Change: D665Y

PolyPhen 2 Score 0.974 (Sensitivity: 0.76; Specificity: 0.96)
Predicted Effect noncoding transcript
Transcript: ENSMUST00000218876
Predicted Effect probably benign
Transcript: ENSMUST00000219387
Meta Mutation Damage Score 0.3497 question?
Coding Region Coverage
  • 1x: 99.9%
  • 3x: 99.7%
  • 10x: 98.7%
  • 20x: 96.5%
Validation Efficiency 100% (61/61)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a coiled-coil domain containing protein. The encoded protein may play a critical role in actin-cytoskeletal reorganization during facial morphogenesis. Mutations in this gene are a cause of oblique facial clefting-1. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. A read-through transcript composed of SPECC1L (sperm antigen with calponin homology and coiled-coil domains 1-like) and the downstream ADORA2A (adenosine A2a receptor) gene sequence has been identified, but it is thought to be non-coding. [provided by RefSeq, Jun 2013]
PHENOTYPE: Homozygous knockout affects cranial neural crest cell migration, which causes neural tube closure defects and leads to embryonic lethality. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 61 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
1700113H08Rik T C 10: 87,061,913 (GRCm39) I121T probably benign Het
4921524L21Rik T A 18: 6,626,399 (GRCm39) M137K possibly damaging Het
Angpt4 C A 2: 151,771,354 (GRCm39) N223K probably benign Het
Ankrd6 T C 4: 32,810,266 (GRCm39) R437G probably damaging Het
Atp9a C T 2: 168,518,093 (GRCm39) S264N probably damaging Het
AY358078 A C 14: 52,063,749 (GRCm39) Y465S probably damaging Het
Bin3 G A 14: 70,374,676 (GRCm39) R235Q probably benign Het
Bsn G A 9: 107,984,554 (GRCm39) P3167S unknown Het
Camk2g G A 14: 20,787,443 (GRCm39) R274C probably damaging Het
Ccdc61 A T 7: 18,643,914 (GRCm39) probably null Het
Ccnjl A T 11: 43,476,165 (GRCm39) T263S probably benign Het
Col17a1 G T 19: 47,641,818 (GRCm39) P944T possibly damaging Het
Cyp2c39 A T 19: 39,501,615 (GRCm39) probably null Het
Cyp2c39 G T 19: 39,501,616 (GRCm39) probably null Het
Cyp4a32 T C 4: 115,459,560 (GRCm39) V98A possibly damaging Het
Dnah9 A G 11: 65,928,519 (GRCm39) V2050A probably damaging Het
F5 A G 1: 164,019,520 (GRCm39) N665S probably benign Het
Fbxl6 A T 15: 76,420,054 (GRCm39) C520S probably damaging Het
Fscn2 C A 11: 120,252,853 (GRCm39) H107N probably damaging Het
Gfm2 C T 13: 97,299,461 (GRCm39) T367M probably damaging Het
Gle1 C G 2: 29,826,127 (GRCm39) P69A probably benign Het
Gpr156 A T 16: 37,807,881 (GRCm39) D176V probably damaging Het
Grip2 A G 6: 91,742,369 (GRCm39) S895P possibly damaging Het
Hfm1 C T 5: 106,989,504 (GRCm39) G1404D probably benign Het
Ifit1bl1 G A 19: 34,571,570 (GRCm39) R296* probably null Het
Ighv1-39 C T 12: 114,878,479 (GRCm39) V31M possibly damaging Het
Itgav A G 2: 83,632,380 (GRCm39) E956G probably damaging Het
Katnip C A 7: 125,352,159 (GRCm39) D26E probably damaging Het
Lsm8 A G 6: 18,853,644 (GRCm39) D86G probably damaging Het
Mdh1b T G 1: 63,754,398 (GRCm39) H390P possibly damaging Het
Mtrf1l A T 10: 5,767,468 (GRCm39) I216N possibly damaging Het
Muc16 G A 9: 18,566,222 (GRCm39) T2099I unknown Het
Myh7 T C 14: 55,221,149 (GRCm39) R925G probably damaging Het
Myo1h T A 5: 114,489,769 (GRCm39) I658N probably damaging Het
Myo5a A T 9: 75,097,195 (GRCm39) D81V possibly damaging Het
Nell1 G A 7: 49,625,171 (GRCm39) C12Y possibly damaging Het
Obscn T C 11: 58,944,522 (GRCm39) Y4724C probably damaging Het
Or8k53 A G 2: 86,177,892 (GRCm39) Y73H probably damaging Het
Pah G A 10: 87,412,049 (GRCm39) D315N probably damaging Het
Per2 A G 1: 91,376,444 (GRCm39) V143A probably damaging Het
Plcxd1 T C 5: 110,248,165 (GRCm39) V38A probably benign Het
Pld1 A G 3: 28,184,896 (GRCm39) probably benign Het
Plekhh2 A G 17: 84,883,215 (GRCm39) N761S probably benign Het
Polh T C 17: 46,493,664 (GRCm39) I318V probably benign Het
Prex1 T C 2: 166,414,880 (GRCm39) Q1323R probably null Het
Rb1cc1 T A 1: 6,333,481 (GRCm39) S1440T probably benign Het
Rbm19 G T 5: 120,265,105 (GRCm39) W382L possibly damaging Het
Rchy1 T C 5: 92,105,801 (GRCm39) D49G probably benign Het
Ric1 A G 19: 29,581,485 (GRCm39) D1402G probably benign Het
S1pr3 G T 13: 51,573,067 (GRCm39) A83S probably damaging Het
S1pr3 C A 13: 51,573,068 (GRCm39) A83D probably damaging Het
Selplg G A 5: 113,958,210 (GRCm39) P32L probably benign Het
Serpinb9c T C 13: 33,333,978 (GRCm39) R355G probably damaging Het
Slx4 G C 16: 3,808,714 (GRCm39) Q409E probably benign Het
Sntg1 A C 1: 8,653,508 (GRCm39) L243R possibly damaging Het
Spen C T 4: 141,198,944 (GRCm39) V3228I possibly damaging Het
Strip1 T C 3: 107,535,516 (GRCm39) E69G probably damaging Het
Tasp1 C A 2: 139,793,457 (GRCm39) V240L probably damaging Het
Tdrd9 T A 12: 112,001,042 (GRCm39) F787L probably damaging Het
Vmn1r228 A G 17: 20,997,144 (GRCm39) S125P probably damaging Het
Wdhd1 A G 14: 47,489,379 (GRCm39) M718T probably damaging Het
Other mutations in Specc1l
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00549:Specc1l APN 10 75,082,055 (GRCm39) missense probably benign 0.12
IGL01638:Specc1l APN 10 75,082,039 (GRCm39) nonsense probably null
IGL01970:Specc1l APN 10 75,081,595 (GRCm39) missense probably damaging 1.00
IGL02539:Specc1l APN 10 75,103,342 (GRCm39) missense probably benign 0.39
IGL02737:Specc1l APN 10 75,082,158 (GRCm39) missense probably damaging 0.99
IGL02941:Specc1l APN 10 75,077,022 (GRCm39) missense probably benign 0.10
R0305:Specc1l UTSW 10 75,081,663 (GRCm39) missense probably damaging 1.00
R0374:Specc1l UTSW 10 75,084,293 (GRCm39) missense probably damaging 0.99
R0402:Specc1l UTSW 10 75,082,260 (GRCm39) missense probably damaging 1.00
R1456:Specc1l UTSW 10 75,082,118 (GRCm39) missense probably damaging 0.98
R1508:Specc1l UTSW 10 75,143,072 (GRCm39) missense probably benign 0.00
R1861:Specc1l UTSW 10 75,145,693 (GRCm39) missense probably damaging 1.00
R1869:Specc1l UTSW 10 75,097,659 (GRCm39) missense probably damaging 1.00
R1929:Specc1l UTSW 10 75,081,438 (GRCm39) missense probably damaging 1.00
R1930:Specc1l UTSW 10 75,145,658 (GRCm39) missense probably damaging 1.00
R2021:Specc1l UTSW 10 75,103,425 (GRCm39) critical splice donor site probably null
R2209:Specc1l UTSW 10 75,082,410 (GRCm39) missense probably damaging 1.00
R2271:Specc1l UTSW 10 75,081,438 (GRCm39) missense probably damaging 1.00
R2937:Specc1l UTSW 10 75,094,965 (GRCm39) missense probably damaging 0.98
R4415:Specc1l UTSW 10 75,082,162 (GRCm39) missense possibly damaging 0.92
R4758:Specc1l UTSW 10 75,082,182 (GRCm39) missense probably damaging 0.99
R5344:Specc1l UTSW 10 75,082,007 (GRCm39) missense possibly damaging 0.84
R5383:Specc1l UTSW 10 75,082,539 (GRCm39) missense possibly damaging 0.86
R5426:Specc1l UTSW 10 75,103,384 (GRCm39) missense probably benign 0.21
R5774:Specc1l UTSW 10 75,081,234 (GRCm39) missense probably damaging 1.00
R5788:Specc1l UTSW 10 75,112,755 (GRCm39) missense probably damaging 1.00
R6101:Specc1l UTSW 10 75,084,466 (GRCm39) missense probably damaging 1.00
R6105:Specc1l UTSW 10 75,084,466 (GRCm39) missense probably damaging 1.00
R6136:Specc1l UTSW 10 75,082,494 (GRCm39) missense probably benign 0.38
R6459:Specc1l UTSW 10 75,082,001 (GRCm39) missense probably damaging 1.00
R6641:Specc1l UTSW 10 75,082,383 (GRCm39) missense probably damaging 1.00
R6996:Specc1l UTSW 10 75,082,113 (GRCm39) missense probably benign 0.23
R7100:Specc1l UTSW 10 75,081,329 (GRCm39) missense probably benign 0.21
R7475:Specc1l UTSW 10 75,082,281 (GRCm39) missense possibly damaging 0.59
R7545:Specc1l UTSW 10 75,080,921 (GRCm39) missense probably benign 0.00
R7615:Specc1l UTSW 10 75,099,120 (GRCm39) missense probably benign 0.02
R7635:Specc1l UTSW 10 75,112,638 (GRCm39) missense probably damaging 1.00
R7640:Specc1l UTSW 10 75,093,703 (GRCm39) missense probably damaging 1.00
R7682:Specc1l UTSW 10 75,081,636 (GRCm39) missense probably damaging 0.99
R7711:Specc1l UTSW 10 75,066,642 (GRCm39) missense probably benign 0.02
R7742:Specc1l UTSW 10 75,082,251 (GRCm39) missense probably benign 0.01
R7847:Specc1l UTSW 10 75,145,670 (GRCm39) missense probably damaging 0.99
R8015:Specc1l UTSW 10 75,076,902 (GRCm39) missense probably benign 0.17
R8030:Specc1l UTSW 10 75,084,389 (GRCm39) missense probably damaging 1.00
R8882:Specc1l UTSW 10 75,065,689 (GRCm39) start codon destroyed unknown
R9069:Specc1l UTSW 10 75,066,640 (GRCm39) missense probably benign 0.03
R9790:Specc1l UTSW 10 75,066,603 (GRCm39) missense probably benign 0.21
R9791:Specc1l UTSW 10 75,066,603 (GRCm39) missense probably benign 0.21
X0021:Specc1l UTSW 10 75,109,874 (GRCm39) missense probably benign
Predicted Primers PCR Primer
(F):5'- GGCTAGGTTGTCAGTCAGTC -3'
(R):5'- AGAACTGCTATTTTCACCACGG -3'

Sequencing Primer
(F):5'- CAGTCAGTCTGTCCGTAGCTG -3'
(R):5'- GCTATTTTCACCACGGAGCAC -3'
Posted On 2018-04-27