Mutagenetix > Incidental Mutation

Incidental Mutation 'R3870:Cc2d2a'

276497

Institutional Source

Beutler Lab

Gene Symbol

Cc2d2a

Ensembl Gene

ENSMUSG00000039765

Gene Name

coiled-coil and C2 domain containing 2A

Synonyms

b2b1035Clo, 5730509K17Rik

MMRRC Submission

040789-MU

Accession Numbers

Genbank: NM_172274; MGI: 1924487

Is this an essential gene?

Probably essential (E-score: 0.912) question?

Stock #

R3870 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

43662346-43740972 bp(+) (GRCm38)

Type of Mutation

nonsense

DNA Base Change (assembly)

C to A at 43718691 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Tyrosine to Stop codon at position 1003 (Y1003*)

Ref Sequence

ENSEMBL: ENSMUSP00000114349 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000048150] [ENSMUST00000125866]

AlphaFold

Q8CFW7

Predicted Effect

probably null
Transcript: ENSMUST00000048150
AA Change: Y1057*

SMART Domains

Protein: ENSMUSP00000048320
Gene: ENSMUSG00000039765
AA Change: Y1057*

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 null
Transcript: ENSMUST00000125866
AA Change: Y1003*

SMART Domains

Protein: ENSMUSP00000114349
Gene: ENSMUSG00000039765
AA Change: Y1003*

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

noncoding transcript
Transcript: ENSMUST00000127355

Meta Mutation Damage Score

0.9754

Coding Region Coverage

1x: 99.2%
3x: 98.7%
10x: 97.6%
20x: 96.1%

Validation Efficiency

90% (61/68)

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: 63 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1700028J19Rik	T	A	7: 44,231,404		probably null	Het
2410089E03Rik	A	T	15: 8,218,464	K1499M	probably damaging	Het
Adam22	C	A	5: 8,132,418	C514F	probably damaging	Het
Akap8	G	A	17: 32,317,839		probably benign	Het
Armcx2	A	T	X: 134,806,299	V195E	probably benign	Het
Atg7	T	C	6: 114,697,047	S301P	possibly damaging	Het
Ccdc93	A	G	1: 121,463,114	S272G	probably benign	Het
Ces1d	C	G	8: 93,175,086	L418F	probably benign	Het
Cntnap5a	A	G	1: 116,060,249	E170G	probably damaging	Het
Crygs	C	T	16: 22,805,551	G102D	possibly damaging	Het
Ehd4	T	A	2: 120,136,953	D120V	probably damaging	Het
Eif4g3	T	A	4: 138,096,900	V71E	probably damaging	Het
Exoc5	A	G	14: 49,019,396		probably benign	Het
Glud1	T	A	14: 34,325,580		probably benign	Het
Gm10985	TTCTCTCTCTCTCTCTCT	TTCTCTCTCTCTCTCT	3: 53,845,205		probably null	Het
Gm11555	G	T	11: 99,649,990	C64*	probably null	Het
Gm5468	A	G	15: 25,414,475		probably benign	Het
Gpatch2	T	A	1: 187,322,294	L74Q	probably damaging	Het
Hnrnpa0	G	A	13: 58,127,899	R139C	probably damaging	Het
Hrh1	A	G	6: 114,480,919	Y387C	probably damaging	Het
Ldb3	A	T	14: 34,567,483	D216E	probably damaging	Het
Lingo1	A	T	9: 56,619,725	S533T	probably benign	Het
Lmtk2	T	G	5: 144,166,427		probably benign	Het
Map1s	A	G	8: 70,917,101	E939G	possibly damaging	Het
Mast1	G	A	8: 84,918,731	T695I	probably damaging	Het
Mettl21e	G	A	1: 44,206,364	R241W	probably benign	Het
Mfsd4a	G	A	1: 132,046,353	T261I	probably damaging	Het
Mmel1	T	C	4: 154,883,638	S144P	probably benign	Het
Myo16	A	T	8: 10,442,239	H727L	probably benign	Het
Ncoa6	T	C	2: 155,415,557		probably null	Het
Nipa2	T	C	7: 55,932,942	R352G	probably damaging	Het
Oaf	C	T	9: 43,222,758	R222Q	probably benign	Het
Olfr701	T	A	7: 106,818,840	Y252*	probably null	Het
Pard3	T	C	8: 127,409,686	S847P	probably damaging	Het
Pgbd1	C	T	13: 21,434,370	R39H	possibly damaging	Het
Plcb1	A	C	2: 135,325,671	I462L	probably damaging	Het
Prex2	T	C	1: 11,160,192	V814A	possibly damaging	Het
Rasal3	G	A	17: 32,393,548	R780W	possibly damaging	Het
Rubcnl	C	T	14: 75,040,916	P380L	probably benign	Het
Ryk	A	G	9: 102,891,228	E359G	probably damaging	Het
Sall2	C	A	14: 52,313,994	L579F	probably damaging	Het
Satb2	A	G	1: 56,891,220	S215P	probably damaging	Het
Scg3	T	C	9: 75,675,499		probably benign	Het
Slc35f5	A	G	1: 125,562,361	T65A	probably benign	Het
Snx33	T	C	9: 56,926,740	N15S	probably benign	Het
Stat2	T	A	10: 128,277,893	S180R	probably benign	Het
Stxbp2	A	G	8: 3,634,079	T129A	probably damaging	Het
Tas1r3	A	T	4: 155,861,353	C529S	probably damaging	Het
Tlr12	T	A	4: 128,616,568	M630L	probably benign	Het
Tnfrsf10b	T	G	14: 69,773,456	D103E	probably benign	Het
Togaram1	A	C	12: 65,002,645	E1285D	probably benign	Het
Tppp	A	G	13: 74,030,772	T111A	probably benign	Het
Trim12c	T	C	7: 104,348,337	Q4R	probably benign	Het
Ttbk2	T	G	2: 120,740,019	S1149R	probably damaging	Het
Uncx	T	C	5: 139,547,365	L395P	probably damaging	Het
Usp14	A	G	18: 10,002,370	S314P	possibly damaging	Het
Usp32	A	T	11: 85,007,055	Y1153*	probably null	Het
Vmn2r6	T	C	3: 64,556,621	E264G	probably damaging	Het
Vmn2r77	T	C	7: 86,811,842	F792S	probably damaging	Het
Vps13c	A	G	9: 67,884,726	I425V	probably benign	Het
Vstm4	C	T	14: 32,863,755	A93V	probably benign	Het
Xrcc6	T	A	15: 82,025,684	S97T	probably benign	Het
Zscan20	A	G	4: 128,586,425	C758R	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
R1881:Cc2d2a	UTSW	5	43740828	missense	probably damaging	0.99
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
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
R8480:Cc2d2a	UTSW	5	43685144	splice site	probably null
R8482:Cc2d2a	UTSW	5	43695239	missense	probably damaging	1.00
R8731:Cc2d2a	UTSW	5	43735446	missense	probably damaging	1.00
R8780:Cc2d2a	UTSW	5	43739350	missense	probably damaging	1.00
R8784:Cc2d2a	UTSW	5	43703303	missense	possibly damaging	0.90
R8871:Cc2d2a	UTSW	5	43699943	missense	possibly damaging	0.71
R8972:Cc2d2a	UTSW	5	43710542	missense	probably benign
R9122:Cc2d2a	UTSW	5	43673739	missense	probably null	0.07
R9125:Cc2d2a	UTSW	5	43703221	missense	probably benign
R9203:Cc2d2a	UTSW	5	43733837	missense	probably benign	0.01
R9310:Cc2d2a	UTSW	5	43695146	missense	probably damaging	1.00
R9343:Cc2d2a	UTSW	5	43718657	missense	probably damaging	1.00
R9353:Cc2d2a	UTSW	5	43703349	critical splice donor site	probably null
Z1177:Cc2d2a	UTSW	5	43703204	missense	probably benign

Predicted Primers

PCR Primer
(F):5'- GACCTTGGAATGTAGTTTAAAAGGCC -3'
(R):5'- ACACCCTTGAGCCTGAGTTG -3'

Sequencing Primer
(F):5'- AGGCCATATGATAACTTTCTAGACC -3'
(R):5'- ACCCTTGAGCCTGAGTTGACTATG -3'

Posted On

2015-04-06