Mutagenetix > Incidental Mutation

Incidental Mutation 'R6046:Cc2d1a'

483299

Institutional Source

Beutler Lab

Gene Symbol

Cc2d1a

Ensembl Gene

ENSMUSG00000036686

Gene Name

coiled-coil and C2 domain containing 1A

Synonyms

Tape, Freud-1

MMRRC Submission

044214-MU

Accession Numbers

Essential gene?

Possibly non essential (E-score: 0.481) question?

Stock #

R6046 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

84859457-84874546 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

G to T at 84863571 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Alanine to Aspartic acid at position 597 (A597D)

Ref Sequence

ENSEMBL: ENSMUSP00000046449 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000040383] [ENSMUST00000093380] [ENSMUST00000117424]

AlphaFold

Q8K1A6

Predicted Effect

possibly damaging
Transcript: ENSMUST00000040383
AA Change: A597D

PolyPhen 2 Score 0.807 (Sensitivity: 0.84; Specificity: 0.93)

SMART Domains

Protein: ENSMUSP00000046449
Gene: ENSMUSG00000036686
AA Change: A597D

Domain	Start	End	E-Value	Type
low complexity region	41	51	N/A	INTRINSIC
low complexity region	83	110	N/A	INTRINSIC
DM14	137	194	1.02e-14	SMART
low complexity region	195	206	N/A	INTRINSIC
low complexity region	229	238	N/A	INTRINSIC
DM14	250	308	8.7e-23	SMART
DM14	342	400	7.44e-31	SMART
low complexity region	457	478	N/A	INTRINSIC
DM14	487	545	4.62e-27	SMART
C2	649	763	5.08e-8	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000093380

SMART Domains

Protein: ENSMUSP00000091073
Gene: ENSMUSG00000012889

Domain	Start	End	E-Value	Type
signal peptide	1	20	N/A	INTRINSIC
LRRNT	38	71	1.91e0	SMART
LRR	70	89	1.81e2	SMART
LRR	90	115	1.76e-1	SMART
LRR	116	139	1.19e2	SMART
LRR	162	186	1.06e1	SMART
LRR	191	210	5.42e1	SMART
LRR	211	231	1.66e1	SMART
LRR	233	257	3.98e1	SMART
LRR_TYP	258	281	7.9e-4	SMART
LRR	304	328	9.24e1	SMART
LRR_TYP	329	352	4.72e-2	SMART
LRR	375	399	2.61e2	SMART
LRR_TYP	400	423	2.61e-4	SMART
LRR	424	444	3.18e1	SMART
LRR	445	470	3.27e1	SMART
LRR_TYP	471	494	3.63e-3	SMART
LRR	495	515	1.97e1	SMART
LRR	516	541	2.03e2	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000117424
AA Change: A551D

PolyPhen 2 Score 0.342 (Sensitivity: 0.90; Specificity: 0.89)

SMART Domains

Protein: ENSMUSP00000112556
Gene: ENSMUSG00000036686
AA Change: A551D

Domain	Start	End	E-Value	Type
low complexity region	41	51	N/A	INTRINSIC
low complexity region	83	110	N/A	INTRINSIC
low complexity region	150	161	N/A	INTRINSIC
low complexity region	184	193	N/A	INTRINSIC
DM14	205	263	8.7e-23	SMART
DM14	297	355	7.44e-31	SMART
low complexity region	411	432	N/A	INTRINSIC
DM14	441	499	4.62e-27	SMART
C2	603	717	5.08e-8	SMART

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000147175

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000154029

Meta Mutation Damage Score

0.1795

Coding Region Coverage

1x: 99.9%
3x: 99.5%
10x: 97.7%
20x: 92.8%

Validation Efficiency

100% (78/78)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a transcriptional repressor that binds to a conserved 14-bp 5'-repressor element and regulates expression of the 5-hydroxytryptamine (serotonin) receptor 1A gene in neuronal cells. The DNA binding and transcriptional repressor activities of the protein are inhibited by calcium. A mutation in this gene results in nonsyndromic mental retardation-3.[provided by RefSeq, Oct 2009]
PHENOTYPE: Mice homozygous for a knock-out allele exhibit partial neonatal lethality, reduced body weight, hunched posture, respiratory distress, increased sensitivity of neurons to hydrogen peroxide, reduced dendrite length, abnormal brain vasculature and reduced synaptic number and density. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 74 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abtb3	T	C	10: 85,223,947 (GRCm39)	V252A	unknown	Het
Actn4	T	C	7: 28,604,044 (GRCm39)	I406V	probably benign	Het
Acyp2	C	T	11: 30,456,354 (GRCm39)	E98K	possibly damaging	Het
Ank1	T	A	8: 23,606,114 (GRCm39)	F1124I	probably damaging	Het
Arhgap44	CTGCT	CTGCTTGCT	11: 64,922,910 (GRCm39)		probably null	Het
Atp9a	C	A	2: 168,476,790 (GRCm39)	V1000L	probably benign	Het
Bnip3	A	G	7: 138,511,033 (GRCm39)		probably benign	Het
Btnl6	T	A	17: 34,727,371 (GRCm39)	R386S	probably damaging	Het
Calcrl	A	G	2: 84,205,658 (GRCm39)	V11A	probably benign	Het
Celsr3	A	G	9: 108,714,350 (GRCm39)	T1960A	probably benign	Het
Cfb	T	A	17: 35,081,078 (GRCm39)		probably null	Het
Chd8	A	G	14: 52,458,528 (GRCm39)	I860T	possibly damaging	Het
Col28a1	A	G	6: 8,168,102 (GRCm39)		probably null	Het
Crhr2	T	A	6: 55,068,277 (GRCm39)	T428S	probably damaging	Het
Crybg2	A	T	4: 133,819,388 (GRCm39)	I1753F	probably damaging	Het
Ctsq	A	T	13: 61,186,955 (GRCm39)	V46E	probably benign	Het
Cxcr1	T	C	1: 74,231,440 (GRCm39)	E194G	probably damaging	Het
Dop1a	A	T	9: 86,397,396 (GRCm39)	H900L	probably damaging	Het
Dpyd	T	A	3: 119,225,224 (GRCm39)	M999K	probably benign	Het
Gbp3	A	C	3: 142,273,560 (GRCm39)	D369A	possibly damaging	Het
Glmp	A	G	3: 88,232,495 (GRCm39)	E36G	probably damaging	Het
Gm10113	T	C	13: 46,330,919 (GRCm39)		noncoding transcript	Het
Gm6486	T	A	5: 3,120,846 (GRCm39)		noncoding transcript	Het
Gm973	T	G	1: 59,671,509 (GRCm39)	L891R	unknown	Het
Heatr3	C	T	8: 88,866,582 (GRCm39)	T8M	probably damaging	Het
Herc1	A	G	9: 66,352,831 (GRCm39)	M2106V	probably damaging	Het
Hfm1	A	T	5: 107,046,509 (GRCm39)		probably null	Het
Hspa14	A	G	2: 3,490,801 (GRCm39)	V462A	possibly damaging	Het
Hspa5	C	A	2: 34,665,761 (GRCm39)	T535K	possibly damaging	Het
Ift140	A	G	17: 25,274,563 (GRCm39)	D745G	probably benign	Het
Ift27	A	T	15: 78,057,981 (GRCm39)	C8S	possibly damaging	Het
Irak1bp1	G	A	9: 82,728,616 (GRCm39)	W182*	probably null	Het
Itga3	A	G	11: 94,953,541 (GRCm39)	I236T	probably benign	Het
Kctd15	T	A	7: 34,349,547 (GRCm39)	N26Y	possibly damaging	Het
Kdm1b	T	C	13: 47,232,729 (GRCm39)	V733A	possibly damaging	Het
Lhx8	A	T	3: 154,027,340 (GRCm39)	L234H	probably damaging	Het
Lrp2	T	A	2: 69,337,098 (GRCm39)	T1225S	probably damaging	Het
Lrrn1	G	A	6: 107,545,488 (GRCm39)	D429N	probably benign	Het
Mettl3	A	T	14: 52,536,243 (GRCm39)	N200K	possibly damaging	Het
Mixl1	G	T	1: 180,524,336 (GRCm39)	A81D	possibly damaging	Het
Mroh2b	T	C	15: 4,980,763 (GRCm39)	I1444T	probably benign	Het
Muc15	T	A	2: 110,561,786 (GRCm39)	L74*	probably null	Het
Olfm2	T	A	9: 20,579,824 (GRCm39)	Y317F	probably damaging	Het
Or52a33	C	T	7: 103,288,886 (GRCm39)	V154M	probably benign	Het
Or5b114-ps1	G	A	19: 13,352,698 (GRCm39)	S124N	probably benign	Het
Or5p54	T	A	7: 107,554,001 (GRCm39)	I51N	probably benign	Het
Pclo	A	T	5: 14,763,302 (GRCm39)	Y3925F	unknown	Het
Pik3c2g	A	T	6: 139,599,137 (GRCm39)	R84S	probably damaging	Het
Pik3c2g	A	G	6: 139,842,518 (GRCm39)	Q449R	probably damaging	Het
Psg28	T	C	7: 18,160,305 (GRCm39)	E297G	probably damaging	Het
Qrich2	A	T	11: 116,337,832 (GRCm39)		probably benign	Het
Rgs9	A	G	11: 109,130,386 (GRCm39)	I363T	probably damaging	Het
Rnpepl1	A	G	1: 92,844,543 (GRCm39)	D345G	probably damaging	Het
Rtn4	T	A	11: 29,658,023 (GRCm39)	F726I	probably damaging	Het
Sart3	A	T	5: 113,893,507 (GRCm39)	I330N	probably damaging	Het
Scn5a	T	C	9: 119,391,440 (GRCm39)	D84G	probably damaging	Het
Sema4a	T	C	3: 88,348,008 (GRCm39)	T438A	probably damaging	Het
Sfxn1	A	C	13: 54,242,961 (GRCm39)	Y73S	probably benign	Het
Slc24a2	A	G	4: 86,914,882 (GRCm39)	M585T	probably damaging	Het
Slc26a7	A	G	4: 14,505,471 (GRCm39)	V656A	probably benign	Het
Smok2a	T	G	17: 13,445,021 (GRCm39)	D199E	probably benign	Het
Tbc1d10c	T	C	19: 4,235,030 (GRCm39)	I344V	probably benign	Het
Tll1	A	T	8: 64,506,925 (GRCm39)	Y605*	probably null	Het
Trim75	G	A	8: 65,435,535 (GRCm39)	P305L	probably damaging	Het
Unc13c	T	C	9: 73,838,166 (GRCm39)	N895S	probably benign	Het
Vmn2r25	A	T	6: 123,799,876 (GRCm39)	I822N	probably damaging	Het
Wasf3	T	G	5: 146,407,166 (GRCm39)	D495E	unknown	Het
Wdhd1	T	A	14: 47,510,667 (GRCm39)	K119*	probably null	Het
Wnt2b	T	A	3: 104,858,339 (GRCm39)	D310V	probably damaging	Het
Zfat	G	T	15: 68,052,626 (GRCm39)	D389E	probably damaging	Het
Zfp282	G	A	6: 47,857,102 (GRCm39)	V112M	probably damaging	Het
Zfp617	A	T	8: 72,687,257 (GRCm39)	K529I	probably damaging	Het
Zfp866	A	T	8: 70,218,373 (GRCm39)	C416S	probably damaging	Het
Zfp991	G	A	4: 147,264,222 (GRCm39)	G533D	probably benign	Het

Other mutations in Cc2d1a

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01078:Cc2d1a	APN	8	84,866,894 (GRCm39)	missense	possibly damaging	0.87
IGL01126:Cc2d1a	APN	8	84,870,033 (GRCm39)	missense	probably benign	0.11
IGL01129:Cc2d1a	APN	8	84,870,033 (GRCm39)	missense	probably benign	0.11
IGL01133:Cc2d1a	APN	8	84,870,033 (GRCm39)	missense	probably benign	0.11
IGL01135:Cc2d1a	APN	8	84,870,033 (GRCm39)	missense	probably benign	0.11
IGL01953:Cc2d1a	APN	8	84,870,607 (GRCm39)	missense	probably benign	0.00
IGL02216:Cc2d1a	APN	8	84,865,942 (GRCm39)	nonsense	probably null
IGL03131:Cc2d1a	APN	8	84,870,056 (GRCm39)	missense	probably damaging	1.00
IGL03268:Cc2d1a	APN	8	84,860,154 (GRCm39)	missense	probably damaging	1.00
IGL03401:Cc2d1a	APN	8	84,861,258 (GRCm39)	missense	probably benign	0.00
Rye	UTSW	8	84,861,599 (GRCm39)	missense	probably damaging	1.00
Taragon	UTSW	8	84,865,166 (GRCm39)	missense	probably damaging	0.96
R0313:Cc2d1a	UTSW	8	84,863,598 (GRCm39)	missense	probably benign	0.38
R0811:Cc2d1a	UTSW	8	84,860,465 (GRCm39)	missense	probably benign	0.23
R0812:Cc2d1a	UTSW	8	84,860,465 (GRCm39)	missense	probably benign	0.23
R0893:Cc2d1a	UTSW	8	84,867,468 (GRCm39)	splice site	probably benign
R1440:Cc2d1a	UTSW	8	84,860,604 (GRCm39)	critical splice donor site	probably null
R1625:Cc2d1a	UTSW	8	84,866,001 (GRCm39)	missense	probably damaging	1.00
R2183:Cc2d1a	UTSW	8	84,867,028 (GRCm39)	missense	probably damaging	1.00
R5155:Cc2d1a	UTSW	8	84,867,755 (GRCm39)	missense	probably benign	0.00
R5959:Cc2d1a	UTSW	8	84,860,132 (GRCm39)	nonsense	probably null
R6386:Cc2d1a	UTSW	8	84,865,166 (GRCm39)	missense	probably damaging	0.96
R6956:Cc2d1a	UTSW	8	84,862,528 (GRCm39)	missense	probably damaging	1.00
R6992:Cc2d1a	UTSW	8	84,861,542 (GRCm39)	missense	probably damaging	1.00
R7156:Cc2d1a	UTSW	8	84,862,389 (GRCm39)	missense	possibly damaging	0.69
R7396:Cc2d1a	UTSW	8	84,870,374 (GRCm39)	splice site	probably null
R7456:Cc2d1a	UTSW	8	84,866,868 (GRCm39)	critical splice donor site	probably null
R7787:Cc2d1a	UTSW	8	84,860,144 (GRCm39)	missense	possibly damaging	0.94
R8507:Cc2d1a	UTSW	8	84,861,605 (GRCm39)	missense	probably benign	0.37
R8808:Cc2d1a	UTSW	8	84,861,599 (GRCm39)	missense	probably damaging	1.00
R9524:Cc2d1a	UTSW	8	84,870,744 (GRCm39)	missense	probably benign	0.06
R9563:Cc2d1a	UTSW	8	84,863,758 (GRCm39)	missense	probably benign	0.14
RF007:Cc2d1a	UTSW	8	84,861,298 (GRCm39)	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- TCCTACTTGATGACACTGAAGGTC -3'
(R):5'- AGGCTTGTCTCAGGAAGCTG -3'

Sequencing Primer
(F):5'- TGAAGGTCCTCTGCTCAAAG -3'
(R):5'- TCTCAGGAAGCTGTGCGTC -3'

Posted On

2017-07-14