Mutagenetix > Incidental Mutations

Incidental Mutation 'R1881:Cc2d2a'

209104

Institutional Source

Beutler Lab

Gene Symbol

Cc2d2a

Ensembl Gene

ENSMUSG00000039765

Gene Name

coiled-coil and C2 domain containing 2A

Synonyms

b2b1035Clo, 5730509K17Rik

MMRRC Submission

039902-MU

Accession Numbers

Genbank: NM_172274; MGI: 1924487

Is this an essential gene?

Probably essential (E-score: 0.887) question?

Stock #

R1881 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

43662346-43740972 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

G to T at 43740828 bp

Zygosity

Heterozygous

Amino Acid Change

Valine to Phenylalanine at position 1626 (V1626F)

Ref Sequence

ENSEMBL: ENSMUSP00000048320 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000047857] [ENSMUST00000048150] [ENSMUST00000114047] [ENSMUST00000119523] [ENSMUST00000125866] [ENSMUST00000196483]

Predicted Effect

probably benign
Transcript: ENSMUST00000047857

SMART Domains

Protein: ENSMUSP00000045792
Gene: ENSMUSG00000039753

Domain	Start	End	E-Value	Type
Pfam:Hemerythrin	6	138	1.3e-10	PFAM
FBOX	208	248	2.31e-9	SMART
low complexity region	289	310	N/A	INTRINSIC
LRR	355	379	2.43e2	SMART
LRR	382	407	4.87e-4	SMART
low complexity region	481	492	N/A	INTRINSIC
LRR	596	621	2.45e0	SMART
LRR	624	649	4.65e-1	SMART
Blast:LRR	650	681	2e-13	BLAST

Predicted Effect

probably damaging
Transcript: ENSMUST00000048150
AA Change: V1626F

PolyPhen 2 Score 0.994 (Sensitivity: 0.69; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000048320
Gene: ENSMUSG00000039765
AA Change: V1626F

Domain	Start	End	E-Value	Type
low complexity region	26	41	N/A	INTRINSIC
low complexity region	58	67	N/A	INTRINSIC
low complexity region	124	136	N/A	INTRINSIC
low complexity region	203	217	N/A	INTRINSIC
coiled coil region	472	501	N/A	INTRINSIC
coiled coil region	553	582	N/A	INTRINSIC
Pfam:CC2D2AN-C2	645	817	2e-36	PFAM
low complexity region	1005	1017	N/A	INTRINSIC
low complexity region	1024	1036	N/A	INTRINSIC
C2	1048	1208	3.43e-5	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000114047

SMART Domains

Protein: ENSMUSP00000109681
Gene: ENSMUSG00000039753

Domain	Start	End	E-Value	Type
Pfam:Hemerythrin	19	132	4.4e-11	PFAM
FBOX	202	242	2.31e-9	SMART
low complexity region	283	304	N/A	INTRINSIC
LRR	349	373	2.43e2	SMART
LRR	376	401	4.87e-4	SMART
low complexity region	475	486	N/A	INTRINSIC
LRR	590	615	2.45e0	SMART
LRR	618	643	4.65e-1	SMART
Blast:LRR	644	675	2e-13	BLAST

Predicted Effect

probably benign
Transcript: ENSMUST00000119523

SMART Domains

Protein: ENSMUSP00000113557
Gene: ENSMUSG00000039753

Domain	Start	End	E-Value	Type
Pfam:Hemerythrin	6	121	2.2e-9	PFAM
FBOX	191	231	2.31e-9	SMART
low complexity region	272	293	N/A	INTRINSIC
LRR	338	362	2.43e2	SMART
LRR	365	390	4.87e-4	SMART
low complexity region	464	475	N/A	INTRINSIC
LRR	579	604	2.45e0	SMART
LRR	607	632	4.65e-1	SMART
Blast:LRR	633	664	2e-13	BLAST

Predicted Effect

probably benign
Transcript: ENSMUST00000125866

SMART Domains

Protein: ENSMUSP00000114349
Gene: ENSMUSG00000039765

Domain	Start	End	E-Value	Type
low complexity region	9	18	N/A	INTRINSIC
low complexity region	75	87	N/A	INTRINSIC
low complexity region	154	168	N/A	INTRINSIC
coiled coil region	423	452	N/A	INTRINSIC
coiled coil region	504	533	N/A	INTRINSIC
Pfam:CC2D2AN-C2	596	768	7.7e-44	PFAM
low complexity region	970	982	N/A	INTRINSIC
C2	994	1154	2.3e-7	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000141902

SMART Domains

Protein: ENSMUSP00000120338
Gene: ENSMUSG00000039753

Domain	Start	End	E-Value	Type
PDB:3V5Z\|B	2	82	3e-43	PDB
FBOX	129	169	2.31e-9	SMART
low complexity region	210	231	N/A	INTRINSIC
LRR	276	300	2.43e2	SMART
LRR	303	328	4.87e-4	SMART
low complexity region	402	413	N/A	INTRINSIC
LRR	517	542	2.45e0	SMART
LRR	545	570	4.65e-1	SMART
Blast:LRR	571	602	3e-13	BLAST

Predicted Effect

probably benign
Transcript: ENSMUST00000196483

SMART Domains

Protein: ENSMUSP00000143703
Gene: ENSMUSG00000039753

Domain	Start	End	E-Value	Type
Pfam:Hemerythrin	6	138	1.3e-10	PFAM
FBOX	208	248	2.31e-9	SMART
low complexity region	289	309	N/A	INTRINSIC
LRR	354	378	2.43e2	SMART
LRR	381	406	4.87e-4	SMART
low complexity region	480	491	N/A	INTRINSIC
LRR	595	620	2.45e0	SMART
LRR	623	648	4.65e-1	SMART
Blast:LRR	649	680	2e-13	BLAST

Meta Mutation Damage Score

0.1661

Coding Region Coverage

1x: 97.3%
3x: 96.7%
10x: 95.1%
20x: 92.3%

Validation Efficiency

96% (71/74)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a coiled-coil and calcium binding domain protein that appears to play a critical role in cilia formation. Mutations in this gene cause Meckel syndrome type 6, as well as Joubert syndrome type 9. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Sep 2009]
PHENOTYPE: Mice homozygous for a null allele exhibit embryonic lethality with multiorgan defects related to cilia biogenesis. Homozygotes for a gene trap allele show randomized body axis, holoprosencephaly, and microphthalmia. Homozygotes for an ENU-induced allele show heterotaxia, congenital heart anomalies, kidney and eye defects, polydactyly, and cleft palate. [provided by MGI curators]

Allele List at MGI

All alleles(5) : Targeted, other(4) Gene trapped(1)

Other mutations in this stock

Total: 66 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4921501E09Rik	T	A	17: 33,065,284	D848V	probably damaging	Het
Acaca	C	A	11: 84,270,387	Y1026*	probably null	Het
Acaca	T	G	11: 84,300,471		probably benign	Het
Adcy8	C	T	15: 64,806,654	M483I	probably damaging	Het
Adgrb2	G	A	4: 130,010,285	G735S	probably damaging	Het
Akap9	A	G	5: 4,050,173	T2612A	probably benign	Het
Armc1	A	T	3: 19,134,896	S202T	possibly damaging	Het
Arsj	T	C	3: 126,438,837	S411P	probably damaging	Het
Ash1l	T	C	3: 88,981,555	V247A	probably benign	Het
Camta2	T	C	11: 70,672,016	D935G	probably benign	Het
Cpne3	T	A	4: 19,535,266	R255S	probably benign	Het
Cramp1l	A	G	17: 24,977,682		probably benign	Het
Csf2rb2	C	T	15: 78,292,535		probably null	Het
Cstf3	A	T	2: 104,654,218	M396L	probably benign	Het
Ctnnd2	A	G	15: 31,005,081		probably benign	Het
Cul7	A	T	17: 46,651,962	Y173F	probably damaging	Het
Dach1	A	T	14: 97,901,396	M537K	probably benign	Het
Ddhd2	T	C	8: 25,727,700	I717V	probably damaging	Het
Dnm1	C	T	2: 32,323,730	V475I	probably damaging	Het
Dnm3	C	T	1: 162,477,948		probably benign	Het
Dsg1c	T	A	18: 20,272,540		probably benign	Het
Eaf2	A	T	16: 36,800,579		probably benign	Het
En1	T	A	1: 120,603,175	V48E	unknown	Het
Eral1	T	A	11: 78,076,049	H180L	possibly damaging	Het
Fry	T	A	5: 150,478,046	C2760S	probably damaging	Het
Gtf2h3	C	T	5: 124,584,273	A113V	probably benign	Het
Hmcn1	C	T	1: 150,638,900	V3574M	probably benign	Het
Ifnl2	T	A	7: 28,509,687	R68W	probably damaging	Het
Il6st	A	G	13: 112,504,413	T908A	probably damaging	Het
Krtap4-1	C	T	11: 99,628,164	G7S	probably null	Het
Ly75	T	C	2: 60,349,940	E631G	probably benign	Het
Mup5	C	A	4: 61,834,631	E52*	probably null	Het
Myh15	A	G	16: 49,071,083	I189V	probably damaging	Het
Nav3	T	A	10: 109,852,559	Q619L	probably damaging	Het
Olfr298	T	C	7: 86,489,438	M38V	probably benign	Het
Olfr513	T	C	7: 108,755,128	S91P	probably damaging	Het
Olfr59	A	T	11: 74,288,666	T7S	probably benign	Het
Olfr733	A	G	14: 50,299,015	I98T	probably damaging	Het
Pam	T	C	1: 97,923,151	T161A	probably benign	Het
Pigs	T	C	11: 78,341,756	V472A	probably benign	Het
Plek	A	T	11: 16,990,111	N176K	probably benign	Het
Poc5	A	G	13: 96,398,731	N168S	probably benign	Het
Pomt2	G	T	12: 87,135,596	A219D	probably damaging	Het
Rttn	T	A	18: 89,015,212	S716T	probably damaging	Het
Sema4b	A	T	7: 80,216,792	S207C	probably damaging	Het
Slc25a20	G	A	9: 108,680,209		probably null	Het
Slc5a6	A	T	5: 31,036,811	L634Q	probably damaging	Het
Slfn3	A	G	11: 83,213,376	I235V	possibly damaging	Het
Smarcc1	T	A	9: 110,175,099	L407Q	probably damaging	Het
Spata32	T	C	11: 103,210,735		probably benign	Het
Tdrd3	A	G	14: 87,486,347		probably null	Het
Thada	A	G	17: 84,436,702	V726A	probably benign	Het
Tmed7	A	T	18: 46,588,555		probably null	Het
Tmem161a	G	A	8: 70,180,785	G94S	probably null	Het
Tmem81	T	A	1: 132,508,210		probably benign	Het
Trim63	C	A	4: 134,316,391	A55E	probably damaging	Het
Trmt1	A	C	8: 84,689,267		probably benign	Het
Trpv4	C	T	5: 114,623,626	V814M	probably benign	Het
Tshz3	T	C	7: 36,771,654	S1023P	possibly damaging	Het
Upk3bl	G	A	5: 136,057,303	R31Q	probably benign	Het
Usp40	T	C	1: 87,994,271	D290G	probably benign	Het
Vmn1r192	G	T	13: 22,187,594	A152E	probably benign	Het
Vmn1r26	T	A	6: 58,008,665	T180S	probably benign	Het
Wdr48	G	T	9: 119,909,540	V89L	probably benign	Het
Wdr6	G	T	9: 108,573,179		probably null	Het
Zfp345	A	G	2: 150,472,355	Y421H	probably damaging	Het

Other mutations in Cc2d2a

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00392:Cc2d2a	APN	5	43724380	splice site	probably benign
IGL00937:Cc2d2a	APN	5	43688122	critical splice acceptor site	probably null
IGL01322:Cc2d2a	APN	5	43689003	missense	probably benign	0.00
IGL01349:Cc2d2a	APN	5	43723784	missense	probably benign	0.01
IGL01448:Cc2d2a	APN	5	43684185	missense	possibly damaging	0.65
IGL01871:Cc2d2a	APN	5	43688969	missense	probably damaging	0.98
IGL01947:Cc2d2a	APN	5	43688237	missense	probably damaging	0.96
IGL01976:Cc2d2a	APN	5	43683115	missense	probably benign	0.02
IGL02113:Cc2d2a	APN	5	43685248	splice site	probably null
IGL02364:Cc2d2a	APN	5	43735450	missense	probably damaging	1.00
IGL02448:Cc2d2a	APN	5	43683205	splice site	probably benign
IGL02458:Cc2d2a	APN	5	43718554	missense	probably benign	0.01
IGL02542:Cc2d2a	APN	5	43688910	splice site	probably benign
IGL02834:Cc2d2a	APN	5	43714521	nonsense	probably null
IGL02940:Cc2d2a	APN	5	43728294	splice site	probably null
IGL03003:Cc2d2a	APN	5	43671266	missense	probably benign	0.22
IGL03183:Cc2d2a	APN	5	43732379	missense	probably damaging	1.00
C9142:Cc2d2a	UTSW	5	43735457	splice site	probably benign
P0028:Cc2d2a	UTSW	5	43684199	missense	probably benign
R0193:Cc2d2a	UTSW	5	43736118	missense	probably damaging	1.00
R0201:Cc2d2a	UTSW	5	43737512	missense	probably damaging	1.00
R0211:Cc2d2a	UTSW	5	43688266	splice site	probably null
R0243:Cc2d2a	UTSW	5	43696638	splice site	probably benign
R0317:Cc2d2a	UTSW	5	43706901	critical splice donor site	probably null
R0453:Cc2d2a	UTSW	5	43703294	missense	probably benign	0.00
R0558:Cc2d2a	UTSW	5	43724387	splice site	probably benign
R0624:Cc2d2a	UTSW	5	43730029	missense	probably benign
R0634:Cc2d2a	UTSW	5	43681381	splice site	probably benign
R1503:Cc2d2a	UTSW	5	43695239	missense	probably damaging	1.00
R1635:Cc2d2a	UTSW	5	43722470	missense	probably damaging	1.00
R1686:Cc2d2a	UTSW	5	43739371	missense	possibly damaging	0.81
R1707:Cc2d2a	UTSW	5	43723688	splice site	probably null
R1715:Cc2d2a	UTSW	5	43718661	missense	probably damaging	0.97
R1765:Cc2d2a	UTSW	5	43714531	missense	probably damaging	0.99
R1794:Cc2d2a	UTSW	5	43688252	missense	probably damaging	1.00
R1917:Cc2d2a	UTSW	5	43706222	missense	probably damaging	1.00
R2005:Cc2d2a	UTSW	5	43726373	critical splice donor site	probably null
R2201:Cc2d2a	UTSW	5	43684033	splice site	probably benign
R2244:Cc2d2a	UTSW	5	43732433	missense	probably damaging	1.00
R2368:Cc2d2a	UTSW	5	43703888	missense	probably benign
R2442:Cc2d2a	UTSW	5	43671305	critical splice donor site	probably null
R2511:Cc2d2a	UTSW	5	43735395	missense	probably damaging	0.99
R3023:Cc2d2a	UTSW	5	43685251	splice site	probably null
R3147:Cc2d2a	UTSW	5	43709155	missense	probably damaging	1.00
R3148:Cc2d2a	UTSW	5	43709155	missense	probably damaging	1.00
R3426:Cc2d2a	UTSW	5	43736109	missense	probably benign	0.00
R3609:Cc2d2a	UTSW	5	43712326	missense	probably damaging	0.99
R3610:Cc2d2a	UTSW	5	43712326	missense	probably damaging	0.99
R3611:Cc2d2a	UTSW	5	43712326	missense	probably damaging	0.99
R3839:Cc2d2a	UTSW	5	43718714	missense	probably benign
R3870:Cc2d2a	UTSW	5	43718691	nonsense	probably null
R4334:Cc2d2a	UTSW	5	43683134	missense	probably benign	0.00
R4913:Cc2d2a	UTSW	5	43739323	missense	probably benign	0.12
R5179:Cc2d2a	UTSW	5	43688221	missense	possibly damaging	0.82
R5315:Cc2d2a	UTSW	5	43720433	missense	probably damaging	0.99
R5352:Cc2d2a	UTSW	5	43706213	missense	probably damaging	1.00
R5386:Cc2d2a	UTSW	5	43730041	missense	probably benign	0.01
R5538:Cc2d2a	UTSW	5	43695176	missense	possibly damaging	0.94
R5568:Cc2d2a	UTSW	5	43709091	missense	probably damaging	0.99
R5618:Cc2d2a	UTSW	5	43729907	missense	probably benign	0.00
R5653:Cc2d2a	UTSW	5	43722462	missense	possibly damaging	0.81
R5817:Cc2d2a	UTSW	5	43712418	missense	probably damaging	1.00
R5858:Cc2d2a	UTSW	5	43715775	missense	probably damaging	1.00
R5905:Cc2d2a	UTSW	5	43712426	missense	probably benign
R5912:Cc2d2a	UTSW	5	43720430	missense	probably damaging	0.97
R6073:Cc2d2a	UTSW	5	43729975	missense	probably damaging	1.00
R6084:Cc2d2a	UTSW	5	43668673	missense	probably benign
R6142:Cc2d2a	UTSW	5	43703198	missense	probably damaging	0.97
R6176:Cc2d2a	UTSW	5	43709113	missense	probably benign	0.32
R6238:Cc2d2a	UTSW	5	43671235	missense	probably benign	0.11
R6381:Cc2d2a	UTSW	5	43715776	missense	possibly damaging	0.69
R6404:Cc2d2a	UTSW	5	43704074	missense	possibly damaging	0.58
R6455:Cc2d2a	UTSW	5	43739412	missense	possibly damaging	0.69
R6695:Cc2d2a	UTSW	5	43718677	missense	probably damaging	0.99
R6805:Cc2d2a	UTSW	5	43681331	missense	probably damaging	1.00
R6919:Cc2d2a	UTSW	5	43703215	missense	probably benign	0.19
R6970:Cc2d2a	UTSW	5	43718585	missense	probably damaging	1.00
R7024:Cc2d2a	UTSW	5	43733929	missense	probably benign	0.10
R7054:Cc2d2a	UTSW	5	43699979	nonsense	probably null
R7071:Cc2d2a	UTSW	5	43709113	missense	probably benign	0.13
R7098:Cc2d2a	UTSW	5	43683139	missense	probably benign	0.00
R7366:Cc2d2a	UTSW	5	43729990	missense	probably damaging	1.00
R7908:Cc2d2a	UTSW	5	43706846	missense	probably benign	0.00
R7920:Cc2d2a	UTSW	5	43739309	missense	probably benign	0.09
R7950:Cc2d2a	UTSW	5	43695296	critical splice donor site	probably null
R8007:Cc2d2a	UTSW	5	43706100	missense	possibly damaging	0.71
R8117:Cc2d2a	UTSW	5	43712439	missense	probably damaging	1.00
R8123:Cc2d2a	UTSW	5	43710554	missense	probably benign
R8179:Cc2d2a	UTSW	5	43699953	missense	probably damaging	0.96
R8279:Cc2d2a	UTSW	5	43736145	missense	probably benign	0.01
R8293:Cc2d2a	UTSW	5	43688228	missense	probably damaging	0.97
R8482:Cc2d2a	UTSW	5	43695239	missense	probably damaging	1.00
Z1177:Cc2d2a	UTSW	5	43703204	missense	probably benign

Predicted Primers

PCR Primer
(F):5'- AACCTCATGATCCTCAAGGC -3'
(R):5'- AGTCAGGTAGTGTCACGAGG -3'

Sequencing Primer
(F):5'- ACAAATATGTTCTTTCTCCTCAGTTC -3'
(R):5'- TAGTGTCACGAGGAGACAGAC -3'

Posted On

2014-06-30