Mutagenetix > Incidental Mutation

Incidental Mutation 'R6992:Cc2d1a'

543910

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

045098-MU

Accession Numbers

Essential gene?

Possibly non essential (E-score: 0.477) question?

Stock #

R6992 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

84859457-84874546 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to T at 84861542 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Valine to Aspartic acid at position 714 (V714D)

Ref Sequence

ENSEMBL: ENSMUSP00000112556 (fasta)

Gene Model

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

AlphaFold

Q8K1A6

Predicted Effect

probably damaging
Transcript: ENSMUST00000040383
AA Change: V760D

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000046449
Gene: ENSMUSG00000036686
AA Change: V760D

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 damaging
Transcript: ENSMUST00000117424
AA Change: V714D

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000112556
Gene: ENSMUSG00000036686
AA Change: V714D

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

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.7%
20x: 98.9%

Validation Efficiency

100% (64/64)

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: 63 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4921539E11Rik	C	T	4: 103,099,990 (GRCm39)	S171N	possibly damaging	Het
6030468B19Rik	T	G	11: 117,688,594 (GRCm39)	M1R	probably null	Het
A730049H05Rik	T	C	6: 92,804,975 (GRCm39)		probably benign	Het
AC125199.3	G	T	16: 88,608,915 (GRCm39)	H52Q	possibly damaging	Het
Adam34	A	T	8: 44,105,642 (GRCm39)	M1K	probably null	Het
Adgrf5	T	C	17: 43,763,214 (GRCm39)		probably null	Het
Antxr2	T	C	5: 98,108,564 (GRCm39)	T316A	probably benign	Het
Cd96	A	G	16: 45,870,087 (GRCm39)	S461P	possibly damaging	Het
Cdc16	C	A	8: 13,809,188 (GRCm39)	A51E	probably benign	Het
Chd4	T	A	6: 125,091,339 (GRCm39)	D1243E	probably benign	Het
Cntf	A	T	19: 12,742,697 (GRCm39)	I21N	probably damaging	Het
Col11a2	C	T	17: 34,266,118 (GRCm39)	A282V	probably benign	Het
Col14a1	T	A	15: 55,274,958 (GRCm39)		probably null	Het
Cyp2b9	T	C	7: 25,900,564 (GRCm39)	Y401H	probably benign	Het
Dlgap4	A	G	2: 156,590,860 (GRCm39)		probably null	Het
Fancd2	T	C	6: 113,547,979 (GRCm39)		probably null	Het
Fcgbpl1	T	A	7: 27,839,608 (GRCm39)	F474I	probably benign	Het
Frem1	A	G	4: 82,858,599 (GRCm39)	V1622A	possibly damaging	Het
Golm1	ACTTCTTCT	ACTTCT	13: 59,797,390 (GRCm39)		probably benign	Het
Gstm4	A	G	3: 107,951,981 (GRCm39)	M3T	possibly damaging	Het
Hdac10	T	C	15: 89,009,534 (GRCm39)	D466G	probably benign	Het
Hook2	A	G	8: 85,729,185 (GRCm39)	E625G	probably damaging	Het
Hspbp1	G	C	7: 4,667,714 (GRCm39)	P260A	probably benign	Het
Igdcc3	C	A	9: 65,088,853 (GRCm39)	Q411K	probably damaging	Het
Il18rap	G	A	1: 40,581,195 (GRCm39)	E356K	probably benign	Het
Inpp4a	A	T	1: 37,428,772 (GRCm39)	M699L	probably damaging	Het
Klhdc1	A	G	12: 69,300,531 (GRCm39)	H157R	probably damaging	Het
Klhl6	G	T	16: 19,772,337 (GRCm39)	T336N	probably damaging	Het
Marchf7	T	C	2: 60,059,428 (GRCm39)		probably null	Het
Mast4	C	T	13: 102,941,155 (GRCm39)	V301I	probably damaging	Het
Mlh3	T	A	12: 85,282,494 (GRCm39)	N1412Y	probably damaging	Het
Mrps27	A	G	13: 99,541,522 (GRCm39)	M209V	probably benign	Het
Mtor	A	T	4: 148,548,932 (GRCm39)	T572S	probably benign	Het
Neurog1	T	C	13: 56,399,363 (GRCm39)	K128R	probably damaging	Het
Or10g6	T	A	9: 39,933,896 (GRCm39)	L69*	probably null	Het
Or2b4	T	A	17: 38,116,754 (GRCm39)	N239K	probably damaging	Het
Or5b122	A	G	19: 13,562,811 (GRCm39)	I48V	possibly damaging	Het
Pcdhgb1	A	G	18: 37,814,652 (GRCm39)	K381R	probably benign	Het
Pdzd2	T	C	15: 12,457,945 (GRCm39)	D306G	probably damaging	Het
Plekha5	C	T	6: 140,489,634 (GRCm39)	T237I	probably damaging	Het
Plscr1l1	T	C	9: 92,236,725 (GRCm39)	M128T	probably benign	Het
Pole	A	T	5: 110,480,365 (GRCm39)	I103F	probably damaging	Het
Ppfia2	A	T	10: 106,310,715 (GRCm39)	Q74L	possibly damaging	Het
Ppm1d	T	C	11: 85,223,178 (GRCm39)	F261S	probably damaging	Het
Psg21	A	T	7: 18,388,668 (GRCm39)		probably null	Het
Ptprg	T	A	14: 11,962,602 (GRCm38)	F133L	probably damaging	Het
Rom1	G	A	19: 8,906,569 (GRCm39)		probably benign	Het
Rtn3	A	G	19: 7,412,489 (GRCm39)	F762L	probably damaging	Het
Sec23ip	T	C	7: 128,367,164 (GRCm39)	S600P	probably benign	Het
Sema4b	T	A	7: 79,869,900 (GRCm39)	I396N	probably damaging	Het
Serpina3k	T	A	12: 104,307,366 (GRCm39)	D199E	probably benign	Het
Slc19a1	A	G	10: 76,885,540 (GRCm39)	D480G	possibly damaging	Het
Slc8b1	G	A	5: 120,665,880 (GRCm39)	V404M	probably damaging	Het
Slco1a4	T	C	6: 141,765,330 (GRCm39)	D304G	probably benign	Het
Smpdl3b	G	T	4: 132,472,452 (GRCm39)	A107D	possibly damaging	Het
Tesk1	A	G	4: 43,447,006 (GRCm39)	T465A	probably benign	Het
Tmem245	A	G	4: 56,937,940 (GRCm39)	F203L	probably benign	Het
Tnip1	T	A	11: 54,809,542 (GRCm39)	I442F	probably benign	Het
Txnip	A	G	3: 96,466,439 (GRCm39)	K127R	possibly damaging	Het
Usp32	A	C	11: 84,922,914 (GRCm39)	L172R	probably damaging	Het
Vmn2r66	A	G	7: 84,654,436 (GRCm39)	S508P	possibly damaging	Het
Vwa5b2	T	A	16: 20,416,952 (GRCm39)	Y550N	probably damaging	Het
Wdr81	G	A	11: 75,342,612 (GRCm39)	A885V	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
R6046:Cc2d1a	UTSW	8	84,863,571 (GRCm39)	missense	possibly damaging	0.81
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
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'- GCGTCCATCCAAAACCTAGG -3'
(R):5'- GTTCAAACTCTGCATCAACCGTG -3'

Sequencing Primer
(F):5'- GTCCATCCAAAACCTAGGTAGGAG -3'
(R):5'- ACCAAGGGCATCAAGTTCG -3'

Posted On

2019-05-13