Mutagenetix > Incidental Mutation

Incidental Mutation 'R0415:Ccdc40'

40264

Institutional Source

Beutler Lab

Gene Symbol

Ccdc40

Ensembl Gene

ENSMUSG00000039963

Gene Name

coiled-coil domain containing 40

Synonyms

B930008I02Rik

MMRRC Submission

038617-MU

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.174) question?

Stock #

R0415 (G1)

Quality Score

216

Status

Validated

Chromosome

Chromosomal Location

119119398-119156064 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 119122944 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Tyrosine to Histidine at position 249 (Y249H)

Ref Sequence

ENSEMBL: ENSMUSP00000062198 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000035935] [ENSMUST00000036113] [ENSMUST00000053440] [ENSMUST00000207655]

AlphaFold

no structure available at present

Predicted Effect

possibly damaging
Transcript: ENSMUST00000035935
AA Change: Y179H

PolyPhen 2 Score 0.861 (Sensitivity: 0.83; Specificity: 0.93)

SMART Domains

Protein: ENSMUSP00000039463
Gene: ENSMUSG00000039963
AA Change: Y179H

Domain	Start	End	E-Value	Type
internal_repeat_1	7	48	1.25e-8	PROSPERO
internal_repeat_1	55	96	1.25e-8	PROSPERO
low complexity region	159	170	N/A	INTRINSIC
low complexity region	208	232	N/A	INTRINSIC
coiled coil region	349	371	N/A	INTRINSIC
coiled coil region	423	447	N/A	INTRINSIC
Blast:HisKA	450	519	3e-13	BLAST
Blast:HisKA	574	629	5e-8	BLAST
low complexity region	793	805	N/A	INTRINSIC
Pfam:BRE1	830	928	4.2e-20	PFAM
coiled coil region	1044	1112	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000036113

SMART Domains

Protein: ENSMUSP00000048516
Gene: ENSMUSG00000039976

Domain	Start	End	E-Value	Type
low complexity region	17	30	N/A	INTRINSIC
Blast:TBC	63	362	5e-75	BLAST
Blast:TBC	373	418	2e-13	BLAST
TBC	421	659	4.39e-43	SMART

Predicted Effect

possibly damaging
Transcript: ENSMUST00000053440
AA Change: Y249H

PolyPhen 2 Score 0.915 (Sensitivity: 0.81; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000062198
Gene: ENSMUSG00000039963
AA Change: Y249H

Domain	Start	End	E-Value	Type
low complexity region	5	27	N/A	INTRINSIC
low complexity region	56	70	N/A	INTRINSIC
internal_repeat_1	79	114	5.57e-8	PROSPERO
internal_repeat_1	111	150	5.57e-8	PROSPERO
low complexity region	229	240	N/A	INTRINSIC
low complexity region	278	302	N/A	INTRINSIC
coiled coil region	419	441	N/A	INTRINSIC
coiled coil region	493	517	N/A	INTRINSIC
Blast:HisKA	520	589	2e-13	BLAST
Blast:HisKA	644	699	4e-8	BLAST
low complexity region	863	875	N/A	INTRINSIC
Pfam:BRE1	900	998	4e-20	PFAM

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000147037

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000150358

Predicted Effect

probably benign
Transcript: ENSMUST00000207655

Meta Mutation Damage Score

0.1795

Coding Region Coverage

1x: 99.1%
3x: 98.4%
10x: 96.7%
20x: 93.6%

Validation Efficiency

97% (99/102)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a protein that is necessary for motile cilia function. It functions in correct left-right axis formation by regulating the assembly of the inner dynein arm and the dynein regulatory complexes, which control ciliary beat. Mutations in this gene cause ciliary dyskinesia type 15, a disorder due to defects in cilia motility. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2011]
PHENOTYPE: Mice homozygous for an ENU-induced allele exhibit heterotaxia, hydrocephalus, short embryonic cilia, and postnatal lethality. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 98 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4933427G23Rik	A	T	5: 24,036,048 (GRCm39)		noncoding transcript	Het
Acox2	A	G	14: 8,243,835 (GRCm38)		probably benign	Het
Adgb	T	C	10: 10,306,811 (GRCm39)		probably null	Het
Adgra3	C	A	5: 50,119,099 (GRCm39)		probably benign	Het
Adgre4	G	A	17: 56,159,288 (GRCm39)	V658I	probably benign	Het
Ahnak	A	G	19: 8,990,235 (GRCm39)		probably benign	Het
Anapc2	A	G	2: 25,168,337 (GRCm39)	T159A	probably damaging	Het
Arfgef3	A	G	10: 18,488,875 (GRCm39)		probably benign	Het
Atf7ip	C	T	6: 136,537,010 (GRCm39)	S81L	possibly damaging	Het
Cacna1i	A	G	15: 80,253,031 (GRCm39)		probably benign	Het
Camk1	A	T	6: 113,318,852 (GRCm39)	Y20*	probably null	Het
Cd109	T	A	9: 78,619,897 (GRCm39)	S1380T	probably benign	Het
Cfap57	A	T	4: 118,426,628 (GRCm39)	L1107Q	possibly damaging	Het
Col6a4	C	T	9: 105,952,279 (GRCm39)	V540I	probably damaging	Het
Cst9	T	A	2: 148,680,362 (GRCm39)		probably benign	Het
Cul5	C	T	9: 53,578,370 (GRCm39)	V73I	probably benign	Het
Cxcl16	T	A	11: 70,349,574 (GRCm39)	K84*	probably null	Het
Cyp2c29	T	C	19: 39,317,539 (GRCm39)		probably benign	Het
D6Ertd527e	C	G	6: 87,088,506 (GRCm39)	T223S	unknown	Het
Dip2c	C	T	13: 9,618,325 (GRCm39)		probably benign	Het
Dis3	A	T	14: 99,324,892 (GRCm39)	I513N	probably damaging	Het
Dnajc16	A	T	4: 141,516,359 (GRCm39)	L3*	probably null	Het
Dop1a	T	A	9: 86,388,555 (GRCm39)	L480M	probably damaging	Het
Eml6	A	G	11: 29,699,392 (GRCm39)	V1787A	possibly damaging	Het
Etnk1	A	G	6: 143,126,500 (GRCm39)	N115S	probably damaging	Het
Fryl	T	C	5: 73,255,757 (GRCm39)	Y758C	probably damaging	Het
Gbp4	G	A	5: 105,268,972 (GRCm39)	R394C	possibly damaging	Het
Ggnbp2	A	C	11: 84,724,051 (GRCm39)		probably benign	Het
Gm7137	A	G	10: 77,624,007 (GRCm39)		probably benign	Het
Gstm2	T	A	3: 107,891,322 (GRCm39)	Q132L	probably benign	Het
Habp2	T	C	19: 56,306,149 (GRCm39)		probably benign	Het
Hectd2	T	C	19: 36,562,284 (GRCm39)		probably benign	Het
Htr6	A	G	4: 138,789,392 (GRCm39)	I291T	possibly damaging	Het
Ighg2c	T	C	12: 113,251,530 (GRCm39)	D199G	unknown	Het
Itih2	A	G	2: 10,110,426 (GRCm39)		probably benign	Het
Kcnab2	A	G	4: 152,479,593 (GRCm39)	F248S	probably benign	Het
Kcnc4	T	C	3: 107,352,749 (GRCm39)	K610E	probably damaging	Het
Kcnk16	T	A	14: 20,313,043 (GRCm39)		probably null	Het
Kndc1	C	T	7: 139,510,037 (GRCm39)	T1293I	probably damaging	Het
Lcp1	A	T	14: 75,464,446 (GRCm39)	I556F	possibly damaging	Het
Lrrc8d	T	C	5: 105,959,731 (GRCm39)	L47P	probably damaging	Het
Lyset	T	A	12: 102,711,135 (GRCm39)	Y119*	probably null	Het
Lyst	T	C	13: 13,886,195 (GRCm39)		probably benign	Het
Macrod2	G	A	2: 142,052,065 (GRCm39)		probably null	Het
Mical2	C	T	7: 111,980,235 (GRCm39)	R70C	probably damaging	Het
Mllt3	ACTGCTGCTGCTGCTGCTGCT	ACTGCTGCTGCTGCTGCT	4: 87,759,576 (GRCm39)		probably benign	Het
Msh3	A	G	13: 92,483,294 (GRCm39)	V283A	possibly damaging	Het
Nup205	T	C	6: 35,191,569 (GRCm39)		probably benign	Het
Nxpe2	T	C	9: 48,237,914 (GRCm39)	T114A	probably damaging	Het
Or51e2	C	T	7: 102,391,294 (GRCm39)	M305I	probably benign	Het
Or5m10	A	T	2: 85,717,782 (GRCm39)	I213F	possibly damaging	Het
Or5m9	A	T	2: 85,877,399 (GRCm39)	H191L	probably benign	Het
Or8c15	A	T	9: 38,121,269 (GRCm39)	M305L	probably benign	Het
Or8g2	A	G	9: 39,821,279 (GRCm39)	Y60C	probably damaging	Het
Pard3	G	A	8: 128,337,047 (GRCm39)	G1221D	probably damaging	Het
Pax5	G	A	4: 44,691,886 (GRCm39)	A120V	probably damaging	Het
Pcsk6	C	T	7: 65,683,622 (GRCm39)	R746C	probably damaging	Het
Pif1	G	A	9: 65,495,333 (GRCm39)	C81Y	probably benign	Het
Plcb1	A	G	2: 135,179,419 (GRCm39)	Y609C	probably damaging	Het
Plcd4	C	A	1: 74,591,256 (GRCm39)	S217Y	probably damaging	Het
Plxna1	G	A	6: 89,334,318 (GRCm39)	H104Y	probably benign	Het
Polr2k	A	G	15: 36,175,602 (GRCm39)	Y45C	probably damaging	Het
Prex1	A	G	2: 166,428,619 (GRCm39)		probably benign	Het
Pth2r	A	G	1: 65,427,598 (GRCm39)	M424V	probably benign	Het
Pygm	A	G	19: 6,441,396 (GRCm39)	R464G	probably benign	Het
Rad51c	A	G	11: 87,288,481 (GRCm39)	L234P	probably damaging	Het
Rnf145	A	G	11: 44,415,965 (GRCm39)	Y60C	probably damaging	Het
Rnf167	T	C	11: 70,540,525 (GRCm39)	I135T	probably damaging	Het
Rnf213	A	T	11: 119,305,295 (GRCm39)	I509F	probably damaging	Het
Ro60	G	T	1: 143,635,813 (GRCm39)	N444K	probably benign	Het
Ryr2	T	C	13: 11,884,042 (GRCm39)	S213G	probably damaging	Het
Selenbp1	T	C	3: 94,844,224 (GRCm39)	V27A	possibly damaging	Het
Selenof	T	G	3: 144,283,453 (GRCm39)	L14R	probably damaging	Het
Sfswap	A	T	5: 129,581,190 (GRCm39)	D121V	probably damaging	Het
Slc25a34	C	A	4: 141,347,780 (GRCm39)	M300I	possibly damaging	Het
Slc34a3	T	G	2: 25,119,122 (GRCm39)	T583P	probably benign	Het
Slc66a3	C	A	12: 17,047,711 (GRCm39)		probably benign	Het
Smg1	C	A	7: 117,781,691 (GRCm39)	A1199S	probably benign	Het
Spint1	A	G	2: 119,076,096 (GRCm39)	T231A	probably damaging	Het
Sptbn1	A	C	11: 30,099,576 (GRCm39)	N229K	probably damaging	Het
Sult2b1	A	G	7: 45,379,516 (GRCm39)		probably benign	Het
Tas2r123	A	T	6: 132,824,801 (GRCm39)	M233L	probably damaging	Het
Tbcel	C	A	9: 42,355,796 (GRCm39)	C139F	probably benign	Het
Thbs2	A	C	17: 14,900,235 (GRCm39)	S573A	probably benign	Het
Tmem132c	A	G	5: 127,640,769 (GRCm39)	E980G	probably damaging	Het
Tmem247	G	T	17: 87,229,750 (GRCm39)	C197F	probably damaging	Het
Tmem43	C	A	6: 91,459,300 (GRCm39)	P257Q	probably benign	Het
Tmprss13	A	G	9: 45,248,430 (GRCm39)		probably null	Het
Ubr5	T	C	15: 37,973,224 (GRCm39)	T2626A	probably damaging	Het
Vmn1r196	T	A	13: 22,478,006 (GRCm39)	V215D	probably damaging	Het
Vmn1r22	G	T	6: 57,877,317 (GRCm39)	T220K	probably benign	Het
Vmn2r116	G	A	17: 23,606,253 (GRCm39)	M388I	possibly damaging	Het
Vmn2r74	A	C	7: 85,610,618 (GRCm39)	C25G	probably damaging	Het
Xndc1	T	C	7: 101,729,823 (GRCm39)		probably benign	Het
Zfp282	A	G	6: 47,874,815 (GRCm39)	D340G	probably damaging	Het
Zfp282	T	A	6: 47,881,987 (GRCm39)	I558N	possibly damaging	Het
Zfp316	T	A	5: 143,250,246 (GRCm39)	T56S	unknown	Het
Zfp345	A	G	2: 150,316,479 (GRCm39)		probably benign	Het

Other mutations in Ccdc40

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01538:Ccdc40	APN	11	119,133,545 (GRCm39)	missense	possibly damaging	0.90
IGL01864:Ccdc40	APN	11	119,133,911 (GRCm39)	missense	probably benign	0.23
IGL01911:Ccdc40	APN	11	119,122,797 (GRCm39)	splice site	probably null
IGL02640:Ccdc40	APN	11	119,128,904 (GRCm39)	missense	probably benign	0.18
IGL03278:Ccdc40	APN	11	119,133,336 (GRCm39)	missense	probably damaging	1.00
IGL03054:Ccdc40	UTSW	11	119,154,027 (GRCm39)	missense	possibly damaging	0.69
PIT4151001:Ccdc40	UTSW	11	119,133,277 (GRCm39)	missense	probably damaging	1.00
R0139:Ccdc40	UTSW	11	119,155,125 (GRCm39)	missense	probably benign	0.00
R0140:Ccdc40	UTSW	11	119,155,125 (GRCm39)	missense	probably benign	0.00
R0617:Ccdc40	UTSW	11	119,133,630 (GRCm39)	missense	probably damaging	1.00
R1396:Ccdc40	UTSW	11	119,122,629 (GRCm39)	missense	possibly damaging	0.66
R1531:Ccdc40	UTSW	11	119,154,015 (GRCm39)	missense	probably benign	0.01
R1751:Ccdc40	UTSW	11	119,121,522 (GRCm39)	critical splice donor site	probably null
R1767:Ccdc40	UTSW	11	119,121,522 (GRCm39)	critical splice donor site	probably null
R1870:Ccdc40	UTSW	11	119,150,730 (GRCm39)	missense	possibly damaging	0.81
R1971:Ccdc40	UTSW	11	119,153,901 (GRCm39)	splice site	probably null
R2106:Ccdc40	UTSW	11	119,155,123 (GRCm39)	missense	probably damaging	1.00
R2370:Ccdc40	UTSW	11	119,153,943 (GRCm39)	missense	probably benign	0.00
R3421:Ccdc40	UTSW	11	119,125,605 (GRCm39)	missense	probably benign	0.02
R3746:Ccdc40	UTSW	11	119,155,252 (GRCm39)	missense	probably benign	0.26
R3749:Ccdc40	UTSW	11	119,155,252 (GRCm39)	missense	probably benign	0.26
R3871:Ccdc40	UTSW	11	119,155,107 (GRCm39)	missense	probably damaging	1.00
R4508:Ccdc40	UTSW	11	119,133,335 (GRCm39)	missense	probably damaging	0.98
R4613:Ccdc40	UTSW	11	119,122,358 (GRCm39)	missense	probably benign	0.09
R4663:Ccdc40	UTSW	11	119,122,332 (GRCm39)	missense	probably benign	0.01
R4787:Ccdc40	UTSW	11	119,144,447 (GRCm39)	missense	possibly damaging	0.74
R4867:Ccdc40	UTSW	11	119,122,614 (GRCm39)	missense	probably benign
R5237:Ccdc40	UTSW	11	119,150,802 (GRCm39)	missense	probably benign	0.00
R5661:Ccdc40	UTSW	11	119,128,753 (GRCm39)	missense	probably benign	0.13
R5678:Ccdc40	UTSW	11	119,122,398 (GRCm39)	missense	possibly damaging	0.61
R5805:Ccdc40	UTSW	11	119,136,906 (GRCm39)	critical splice donor site	probably null
R5830:Ccdc40	UTSW	11	119,133,572 (GRCm39)	missense	probably benign	0.00
R5895:Ccdc40	UTSW	11	119,144,229 (GRCm39)	missense	probably damaging	1.00
R5932:Ccdc40	UTSW	11	119,141,838 (GRCm39)	missense	probably damaging	0.98
R6034:Ccdc40	UTSW	11	119,133,898 (GRCm39)	missense	possibly damaging	0.70
R6034:Ccdc40	UTSW	11	119,133,898 (GRCm39)	missense	possibly damaging	0.70
R6109:Ccdc40	UTSW	11	119,122,804 (GRCm39)	missense	probably benign
R6166:Ccdc40	UTSW	11	119,122,827 (GRCm39)	missense	probably benign
R6336:Ccdc40	UTSW	11	119,122,819 (GRCm39)	missense	possibly damaging	0.82
R6569:Ccdc40	UTSW	11	119,133,560 (GRCm39)	missense	probably damaging	1.00
R6884:Ccdc40	UTSW	11	119,133,565 (GRCm39)	missense	possibly damaging	0.82
R7022:Ccdc40	UTSW	11	119,122,612 (GRCm39)	missense	possibly damaging	0.82
R7212:Ccdc40	UTSW	11	119,155,270 (GRCm39)	missense	probably damaging	0.99
R7472:Ccdc40	UTSW	11	119,153,974 (GRCm39)	missense	probably benign	0.30
R7522:Ccdc40	UTSW	11	119,123,047 (GRCm39)	missense	possibly damaging	0.73
R7888:Ccdc40	UTSW	11	119,119,967 (GRCm39)	missense	unknown
R8041:Ccdc40	UTSW	11	119,122,507 (GRCm39)	missense	possibly damaging	0.53
R8117:Ccdc40	UTSW	11	119,144,211 (GRCm39)	missense	probably benign	0.00
R8162:Ccdc40	UTSW	11	119,150,870 (GRCm39)	critical splice donor site	probably null
R8514:Ccdc40	UTSW	11	119,121,459 (GRCm39)	missense	unknown
R8725:Ccdc40	UTSW	11	119,155,323 (GRCm39)	missense	probably benign
R8727:Ccdc40	UTSW	11	119,155,323 (GRCm39)	missense	probably benign
R8799:Ccdc40	UTSW	11	119,155,292 (GRCm39)	missense	probably benign	0.00
R8877:Ccdc40	UTSW	11	119,153,992 (GRCm39)	missense	probably damaging	1.00
R9304:Ccdc40	UTSW	11	119,122,597 (GRCm39)	missense	probably benign	0.06
S24628:Ccdc40	UTSW	11	119,122,944 (GRCm39)	missense	possibly damaging	0.92
Z1176:Ccdc40	UTSW	11	119,142,834 (GRCm39)	missense	probably damaging	1.00
Z1177:Ccdc40	UTSW	11	119,145,224 (GRCm39)	missense	probably benign	0.16
Z1177:Ccdc40	UTSW	11	119,128,933 (GRCm39)	missense	probably damaging	0.96

Predicted Primers

PCR Primer
(F):5'- AGACGTGGACTCCATTAGGAAGGC -3'
(R):5'- AAACACTCACCGTGCTGTCCTC -3'

Sequencing Primer
(F):5'- CCTCCGAGGAATAGACTTGGAATC -3'
(R):5'- GGCTCATATATGCCTTGCTGGA -3'

Posted On

2013-05-23