Mutagenetix > Incidental Mutation

Incidental Mutation 'R6919:Cc2d2a'

539488

Institutional Source

Beutler Lab

Gene Symbol

Cc2d2a

Ensembl Gene

ENSMUSG00000039765

Gene Name

coiled-coil and C2 domain containing 2A

Synonyms

b2b1035Clo, 5730509K17Rik

MMRRC Submission

Accession Numbers

Genbank: NM_172274; MGI: 1924487

Is this an essential gene?

Probably essential (E-score: 0.912) question?

Stock #

R6919 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

43662346-43740972 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 43703215 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Aspartic acid to Glutamic Acid at position 544 (D544E)

Ref Sequence

ENSEMBL: ENSMUSP00000048320 (fasta)

Gene Model

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

AlphaFold

Q8CFW7

Predicted Effect

probably benign
Transcript: ENSMUST00000048150
AA Change: D544E

PolyPhen 2 Score 0.194 (Sensitivity: 0.92; Specificity: 0.87)

SMART Domains

Protein: ENSMUSP00000048320
Gene: ENSMUSG00000039765
AA Change: D544E

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: ENSMUST00000125866
AA Change: D495E

PolyPhen 2 Score 0.037 (Sensitivity: 0.94; Specificity: 0.82)

SMART Domains

Protein: ENSMUSP00000114349
Gene: ENSMUSG00000039765
AA Change: D495E

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

Meta Mutation Damage Score

0.0708

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.3%
20x: 97.8%

Validation Efficiency

99% (84/85)

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: 83 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1700086D15Rik	A	G	11: 65,152,530		probably benign	Het
4931408C20Rik	T	C	1: 26,682,934	Y1055C	probably benign	Het
6430548M08Rik	T	C	8: 120,145,482	S50P	probably damaging	Het
Aacs	A	G	5: 125,506,163	D261G	probably benign	Het
Abcc4	T	A	14: 118,594,894	T775S	probably benign	Het
Acsl6	A	G	11: 54,341,756		probably null	Het
Agbl5	T	A	5: 30,904,717	F196I	probably benign	Het
Ahnak2	T	C	12: 112,774,684	T985A	possibly damaging	Het
Ak1	A	T	2: 32,631,122	D101V	possibly damaging	Het
Alx1	A	G	10: 103,025,200	Y156H	probably damaging	Het
Angptl7	T	A	4: 148,500,031	S87C	probably benign	Het
Ankrd36	A	G	11: 5,629,299	T188A	probably benign	Het
Arhgap11a	A	C	2: 113,839,709	S356R	possibly damaging	Het
Ascc3	G	T	10: 50,645,753	E455*	probably null	Het
Atp6v0a2	G	A	5: 124,712,161		probably null	Het
B3gnt7	T	C	1: 86,305,694	W104R	probably damaging	Het
Bbs9	G	A	9: 22,812,544		probably null	Het
Cic	C	T	7: 25,271,777	T311I	probably benign	Het
Cngb1	T	A	8: 95,248,375	R1157W	probably null	Het
Cntln	A	G	4: 85,115,368	H1310R	probably benign	Het
Cntnap5c	A	T	17: 58,293,953	I764F	probably benign	Het
Col26a1	T	C	5: 136,744,234	Q362R	possibly damaging	Het
Cyp2c29	G	A	19: 39,291,141	R100K	probably benign	Het
D17H6S53E	C	G	17: 35,127,246	D44E	probably damaging	Het
Dap3	A	G	3: 88,930,989	V65A	probably damaging	Het
Dna2	A	T	10: 62,957,003	I266F	probably damaging	Het
Dnah14	G	A	1: 181,585,066	G57E	probably benign	Het
Dock9	A	T	14: 121,643,152	V333E	probably benign	Het
Dpm1	A	G	2: 168,230,275	Y27H	probably damaging	Het
Dsp	A	T	13: 38,167,655	Y150F	possibly damaging	Het
Emilin3	A	T	2: 160,908,098	I577N	probably damaging	Het
Erap1	A	G	13: 74,671,433	T189A	probably benign	Het
Fam208a	T	A	14: 27,449,801	L397*	probably null	Het
Fat2	A	G	11: 55,282,771	I2372T	possibly damaging	Het
Fbn2	A	T	18: 58,124,187		probably null	Het
Gnl1	A	T	17: 35,987,533	R390*	probably null	Het
Hivep1	A	G	13: 42,183,452	I2336V	probably benign	Het
Il17rb	C	G	14: 30,004,271		probably null	Het
Itga9	T	C	9: 118,887,815	W396R	probably damaging	Het
Katnal2	A	G	18: 77,011,038	V152A	probably benign	Het
Kcnk3	A	G	5: 30,622,400	T265A	probably benign	Het
Klhl1	T	C	14: 96,136,594	Y672C	probably benign	Het
Leng8	C	A	7: 4,143,626	N412K	possibly damaging	Het
Lrrc9	T	A	12: 72,506,393	F1356L	probably benign	Het
Map7	A	G	10: 20,171,082		probably benign	Het
Mei1	T	C	15: 82,081,930	F251S	probably damaging	Het
Mia2	A	G	12: 59,129,895	E9G	possibly damaging	Het
Ms4a13	C	A	19: 11,171,885	W182C	probably benign	Het
Muc16	C	T	9: 18,660,299	R308K	unknown	Het
Olfr1195	G	A	2: 88,683,684	T16I	possibly damaging	Het
Olfr936	A	G	9: 39,047,531		probably benign	Het
Pcnt	A	G	10: 76,385,798	V1998A	probably benign	Het
Pgm1	A	T	5: 64,097,025	N51I	probably benign	Het
Piezo1	T	A	8: 122,490,281	H1333L	probably damaging	Het
Prg2	G	A	2: 84,983,256	V199M	probably damaging	Het
Prss51	T	C	14: 64,097,488	V182A	probably damaging	Het
Psmb9	A	T	17: 34,183,225	Y132*	probably null	Het
Ralyl	T	C	3: 13,777,031	Y76H	probably damaging	Het
Rnaset2a	A	T	17: 8,130,282	D174E	probably benign	Het
Rnft1	G	A	11: 86,495,330		probably null	Het
Robo2	T	C	16: 73,961,867	Y676C	probably damaging	Het
Samd9l	T	G	6: 3,376,313	Y316S	possibly damaging	Het
Siah3	T	A	14: 75,456,138	F28Y	possibly damaging	Het
Slc28a3	C	T	13: 58,573,443		probably null	Het
Slc8a1	A	G	17: 81,388,872	F911S	probably damaging	Het
Speg	T	A	1: 75,387,908	L156*	probably null	Het
Spopl	T	G	2: 23,517,861	M269L	probably benign	Het
Tacr1	C	T	6: 82,557,073	T360I	probably benign	Het
Tmem262	A	G	19: 6,080,737	E95G	probably benign	Het
Tmem68	G	T	4: 3,569,669	T7N	possibly damaging	Het
Top3a	T	A	11: 60,749,493	I460F	probably damaging	Het
Trafd1	G	A	5: 121,384,074	R5*	probably null	Het
Trim16	T	A	11: 62,840,869	V435D	possibly damaging	Het
Tspan17	A	G	13: 54,796,033	D236G	probably damaging	Het
Tssk2	A	T	16: 17,899,701	M323L	probably benign	Het
Ubqln5	A	G	7: 104,129,008	V203A	probably benign	Het
Utrn	A	T	10: 12,693,470	L1134*	probably null	Het
Vmn1r37	C	T	6: 66,731,720	S73F	possibly damaging	Het
Vps13c	A	G	9: 67,927,452	K1688E	probably damaging	Het
Zbtb39	A	G	10: 127,741,842	D95G	probably damaging	Het
Zfhx3	T	A	8: 108,800,528	I1019N	probably damaging	Het
Zfp207	C	T	11: 80,395,503		probably benign	Het
Zmiz1	C	T	14: 25,643,638	T169M	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
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
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'- CACAGGCTAGTTTCTTAACTGTCTG -3'
(R):5'- TCAGGGGTTTGCCTTCCAAG -3'

Sequencing Primer
(F):5'- AACTGTCTGTGTTAATGTCTCTTCAG -3'
(R):5'- TTCCAAGGCCCTCCCTAG -3'

Posted On

2018-11-06