Mutagenetix > Incidental Mutations

Incidental Mutation 'R0499:Pcdh9'

47054

Institutional Source

Beutler Lab

Gene Symbol

Pcdh9

Ensembl Gene

ENSMUSG00000055421

Gene Name

protocadherin 9

Synonyms

C630029H24Rik, A730003J17Rik, C530050I23Rik, LOC382930, 1500001L12Rik

MMRRC Submission

038695-MU

Accession Numbers

Is this an essential gene?

Possibly non essential (E-score: 0.280) question?

Stock #

R0499 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

93013410-93890679 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

G to A at 93886235 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Threonine to Methionine at position 833 (T833M)

Ref Sequence

ENSEMBL: ENSMUSP00000141396 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000068992] [ENSMUST00000192221] [ENSMUST00000193901] [ENSMUST00000194056] [ENSMUST00000195376] [ENSMUST00000195826]

AlphaFold

F8VPK8

Predicted Effect

probably damaging
Transcript: ENSMUST00000068992
AA Change: T833M

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000070935
Gene: ENSMUSG00000055421
AA Change: T833M

Domain	Start	End	E-Value	Type
signal peptide	1	23	N/A	INTRINSIC
CA	49	140	8.37e-3	SMART
CA	164	250	1.01e-20	SMART
CA	274	356	2.34e-25	SMART
CA	386	467	2.14e-19	SMART
CA	491	570	4.27e-28	SMART
CA	594	673	2.45e-28	SMART
CA	700	782	1.01e-6	SMART
transmembrane domain	814	836	N/A	INTRINSIC
low complexity region	858	883	N/A	INTRINSIC

Predicted Effect

probably damaging
Transcript: ENSMUST00000192221
AA Change: T710M

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000142260
Gene: ENSMUSG00000055421
AA Change: T710M

Domain	Start	End	E-Value	Type
CA	41	127	1.01e-20	SMART
CA	151	233	2.34e-25	SMART
CA	263	344	2.14e-19	SMART
CA	368	447	4.27e-28	SMART
CA	471	550	2.45e-28	SMART
CA	577	659	1.01e-6	SMART
transmembrane domain	691	713	N/A	INTRINSIC
low complexity region	735	760	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000192817

Predicted Effect

probably damaging
Transcript: ENSMUST00000193901
AA Change: T833M

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000141759
Gene: ENSMUSG00000055421
AA Change: T833M

Domain	Start	End	E-Value	Type
signal peptide	1	23	N/A	INTRINSIC
CA	49	140	8.37e-3	SMART
CA	164	250	1.01e-20	SMART
CA	274	356	2.34e-25	SMART
CA	386	467	2.14e-19	SMART
CA	491	570	4.27e-28	SMART
CA	594	673	2.45e-28	SMART
CA	700	782	1.01e-6	SMART
transmembrane domain	814	836	N/A	INTRINSIC
low complexity region	858	883	N/A	INTRINSIC

Predicted Effect

probably damaging
Transcript: ENSMUST00000194056
AA Change: T833M

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000141602
Gene: ENSMUSG00000055421
AA Change: T833M

Domain	Start	End	E-Value	Type
signal peptide	1	23	N/A	INTRINSIC
CA	49	140	4.1e-5	SMART
CA	164	250	4.8e-23	SMART
CA	274	356	1.2e-27	SMART
CA	386	467	1.1e-21	SMART
CA	491	570	2e-30	SMART
CA	594	673	1.2e-30	SMART
CA	700	782	4.9e-9	SMART
transmembrane domain	814	836	N/A	INTRINSIC
low complexity region	860	873	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000194129

Predicted Effect

probably damaging
Transcript: ENSMUST00000195376
AA Change: T833M

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000142224
Gene: ENSMUSG00000055421
AA Change: T833M

Domain	Start	End	E-Value	Type
signal peptide	1	23	N/A	INTRINSIC
CA	49	140	4.1e-5	SMART
CA	164	250	4.8e-23	SMART
CA	274	356	1.2e-27	SMART
CA	386	467	1.1e-21	SMART
CA	491	570	2e-30	SMART
CA	594	673	1.2e-30	SMART
CA	700	782	4.9e-9	SMART
transmembrane domain	814	836	N/A	INTRINSIC
low complexity region	858	883	N/A	INTRINSIC

Predicted Effect

probably damaging
Transcript: ENSMUST00000195826
AA Change: T833M

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000141396
Gene: ENSMUSG00000055421
AA Change: T833M

Domain	Start	End	E-Value	Type
signal peptide	1	23	N/A	INTRINSIC
CA	49	140	8.37e-3	SMART
CA	164	250	1.01e-20	SMART
CA	274	356	2.34e-25	SMART
CA	386	467	2.14e-19	SMART
CA	491	570	4.27e-28	SMART
CA	594	673	2.45e-28	SMART
CA	700	782	1.01e-6	SMART
transmembrane domain	814	836	N/A	INTRINSIC
low complexity region	858	883	N/A	INTRINSIC

Meta Mutation Damage Score

0.6467

Coding Region Coverage

1x: 99.2%
3x: 98.5%
10x: 96.8%
20x: 94.2%

Validation Efficiency

99% (97/98)

MGI Phenotype

FUNCTION: This gene encodes a member of the protocadherin family, and cadherin superfamily, of transmembrane proteins containing cadherin domains. These proteins mediate cell adhesion in neural tissues in the presence of calcium. The encoded protein may be involved in signaling at neuronal synaptic junctions. Sharing a characteristic with other protocadherin genes, this gene has a notably large exon that encodes multiple cadherin domains and a transmembrane region. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Nov 2012]
PHENOTYPE: Mice homozygous for a knock-out allele exhibit impaired long-term social and bject recognition and sensorimotor development. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 94 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Acad9	T	C	3: 36,085,415	V388A	probably damaging	Het
Acpp	T	C	9: 104,320,002	E146G	probably damaging	Het
Adap2	A	T	11: 80,176,079	R276S	probably damaging	Het
Agbl3	A	T	6: 34,839,335	M727L	probably benign	Het
Ahnak	T	A	19: 9,000,264		probably benign	Het
Ankmy1	G	T	1: 92,886,226	D410E	probably damaging	Het
Ankra2	T	C	13: 98,266,454	S70P	probably damaging	Het
Aox4	T	C	1: 58,263,397		probably null	Het
Arl13b	G	A	16: 62,801,733	T399I	probably benign	Het
Atad2	A	T	15: 58,103,240	D652E	possibly damaging	Het
Atad2	T	G	15: 58,120,949	M328L	probably benign	Het
BC052040	C	T	2: 115,642,691	R101W	probably damaging	Het
Ccnb1	T	C	13: 100,780,134		probably null	Het
Ccr2	G	C	9: 124,105,939	K85N	possibly damaging	Het
Ccr2	A	T	9: 124,106,126	T148S	possibly damaging	Het
Cdc20b	T	C	13: 113,055,950	V59A	probably benign	Het
Cdkl3	T	C	11: 52,032,416	S507P	possibly damaging	Het
Celf6	C	A	9: 59,602,878	T86K	probably benign	Het
Ces1g	A	G	8: 93,333,689	F101L	probably benign	Het
Cntnap3	C	T	13: 64,858,678	D107N	probably benign	Het
Col15a1	A	T	4: 47,262,950	D534V	probably damaging	Het
Col27a1	A	G	4: 63,300,741		probably benign	Het
Csmd3	T	C	15: 47,847,131	T1687A	probably benign	Het
Cstf3	A	G	2: 104,649,605	I272M	possibly damaging	Het
Cyp2d40	T	C	15: 82,761,217	T150A	probably benign	Het
Dnah8	T	A	17: 30,715,509	F1489L	possibly damaging	Het
Dopey2	A	T	16: 93,770,437	T1251S	probably benign	Het
Dtx2	G	A	5: 136,029,103	G421R	probably damaging	Het
Dusp27	C	A	1: 166,099,101	V981L	probably benign	Het
Epb41l3	T	A	17: 69,247,659	D251E	probably benign	Het
Erg	A	C	16: 95,360,983	Y305*	probably null	Het
Exosc4	G	A	15: 76,329,566	A197T	probably benign	Het
Fam227b	T	A	2: 126,100,909	I323L	probably benign	Het
Far1	G	T	7: 113,554,296		probably benign	Het
Fmod	A	G	1: 134,041,196	I325V	possibly damaging	Het
Fshr	C	G	17: 89,009,285	S169T	probably benign	Het
Gm17359	T	A	3: 79,405,786	W56R	probably damaging	Het
Gm17660	C	A	5: 104,074,881	G24*	probably null	Het
Gm4076	G	T	13: 85,127,226		noncoding transcript	Het
Gm5134	A	T	10: 75,992,525	Y313F	probably benign	Het
H2-Q6	T	A	17: 35,425,203	F54I	probably damaging	Het
Hcrtr2	C	A	9: 76,254,672	L145F	probably damaging	Het
Hepacam2	A	G	6: 3,476,121	L268P	probably damaging	Het
Herc2	C	A	7: 56,184,369	C3107*	probably null	Het
Herc4	T	C	10: 63,264,032	V78A	probably damaging	Het
Hyal5	T	C	6: 24,877,921	W339R	probably damaging	Het
Igfbp6	T	A	15: 102,147,984		probably null	Het
Il18rap	A	T	1: 40,525,058	H112L	probably benign	Het
Il1r2	T	A	1: 40,123,149	Y317*	probably null	Het
Ints8	C	A	4: 11,246,097	V190L	probably benign	Het
Ipo11	T	C	13: 106,925,087	T22A	probably benign	Het
Itgb4	C	A	11: 115,979,695	R117S	probably benign	Het
Lcorl	C	G	5: 45,734,369	G214A	probably benign	Het
Lgals3bp	T	A	11: 118,398,193		probably null	Het
Lyst	T	A	13: 13,616,713	L54I	probably damaging	Het
Mcm9	T	C	10: 53,538,154	T1015A	probably benign	Het
Mef2d	T	A	3: 88,156,518	I84N	probably damaging	Het
Mmrn2	A	G	14: 34,397,956	N261S	probably damaging	Het
Mpdz	T	C	4: 81,292,531	T1693A	probably benign	Het
Mss51	T	A	14: 20,484,688	Q338L	possibly damaging	Het
Mstn	T	A	1: 53,063,984	Y160N	probably damaging	Het
Muc6	T	C	7: 141,640,468	T1431A	probably benign	Het
Nek9	A	T	12: 85,301,883	M959K	probably benign	Het
Odf3l2	T	C	10: 79,640,265	D155G	probably damaging	Het
Olfr1311	A	T	2: 112,021,432	C141S	probably damaging	Het
Olfr319	G	A	11: 58,702,243	V181I	probably benign	Het
Olfr911-ps1	A	T	9: 38,524,505	M258L	probably benign	Het
Otog	G	T	7: 46,273,832	G1044W	probably damaging	Het
Pdcd10	T	C	3: 75,527,651	K111R	probably damaging	Het
Pde5a	A	G	3: 122,748,458	N199S	probably damaging	Het
Plekhg1	T	C	10: 3,937,971	V355A	probably damaging	Het
Podn	G	T	4: 108,021,594	L359I	probably damaging	Het
Psd	T	C	19: 46,322,161	E483G	probably damaging	Het
Ptch2	T	A	4: 117,111,143	L905*	probably null	Het
Rxfp2	T	A	5: 150,066,415	N420K	probably damaging	Het
Sde2	T	A	1: 180,862,427	D237E	probably benign	Het
Serpina1d	A	T	12: 103,765,757	L281Q	probably damaging	Het
Serpina9	T	C	12: 104,001,470	N222S	probably benign	Het
Sh3bgrl2	A	G	9: 83,577,559	K57E	probably damaging	Het
Shc3	C	T	13: 51,480,228		probably benign	Het
Sik3	T	C	9: 46,208,740	M659T	possibly damaging	Het
Slc23a2	A	G	2: 132,072,017	L280P	probably damaging	Het
Smchd1	G	T	17: 71,387,088	Q1221K	probably benign	Het
Spocd1	A	G	4: 129,955,470	N694S	possibly damaging	Het
Tecta	T	C	9: 42,352,063	D1409G	probably damaging	Het
Tmem131	A	T	1: 36,841,673	V172D	probably damaging	Het
Trpm3	T	C	19: 22,986,873	M1244T	possibly damaging	Het
Ugcg	G	C	4: 59,217,036	V187L	possibly damaging	Het
Usp17le	T	C	7: 104,768,501	N478S	probably benign	Het
Usp36	A	G	11: 118,273,571	V205A	probably damaging	Het
Vmn1r25	T	A	6: 57,978,509	Q265L	probably damaging	Het
Vwf	A	T	6: 125,638,114	H1176L	probably benign	Het
Zfyve28	C	T	5: 34,232,206	D217N	possibly damaging	Het
Zranb3	A	C	1: 127,955,080		probably null	Het

Other mutations in Pcdh9

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00482:Pcdh9	APN	14	93326694	missense	probably damaging	1.00
IGL02183:Pcdh9	APN	14	93886284	missense	probably benign	0.01
IGL02244:Pcdh9	APN	14	93326768	missense	probably damaging	1.00
IGL02571:Pcdh9	APN	14	93560587	splice site	probably benign
IGL03018:Pcdh9	APN	14	93015576	missense	probably null
I1329:Pcdh9	UTSW	14	93886209	missense	probably benign	0.00
R0027:Pcdh9	UTSW	14	93888645	missense	probably null	0.99
R0027:Pcdh9	UTSW	14	93888645	missense	probably null	0.99
R0477:Pcdh9	UTSW	14	93887678	missense	probably damaging	0.99
R0787:Pcdh9	UTSW	14	93886757	missense	possibly damaging	0.88
R1205:Pcdh9	UTSW	14	93886065	missense	probably benign	0.01
R1616:Pcdh9	UTSW	14	93886969	nonsense	probably null
R1620:Pcdh9	UTSW	14	93888305	missense	probably damaging	1.00
R1622:Pcdh9	UTSW	14	93885875	missense	probably benign	0.03
R1708:Pcdh9	UTSW	14	93888305	missense	probably damaging	1.00
R1721:Pcdh9	UTSW	14	93888035	missense	probably damaging	1.00
R1753:Pcdh9	UTSW	14	93887225	missense	probably benign	0.33
R1799:Pcdh9	UTSW	14	93888671	missense	probably benign	0.36
R1867:Pcdh9	UTSW	14	93888035	missense	probably damaging	1.00
R1987:Pcdh9	UTSW	14	93888305	missense	probably damaging	1.00
R1988:Pcdh9	UTSW	14	93888305	missense	probably damaging	1.00
R2444:Pcdh9	UTSW	14	93886791	missense	probably benign	0.10
R3895:Pcdh9	UTSW	14	93887538	missense	probably damaging	1.00
R3926:Pcdh9	UTSW	14	93886810	nonsense	probably null
R4166:Pcdh9	UTSW	14	93887520	nonsense	probably null
R4429:Pcdh9	UTSW	14	93887384	missense	probably damaging	0.96
R4589:Pcdh9	UTSW	14	93888192	missense	probably damaging	1.00
R4604:Pcdh9	UTSW	14	93887180	missense	probably damaging	1.00
R4607:Pcdh9	UTSW	14	93015573	missense	probably benign	0.08
R4621:Pcdh9	UTSW	14	93887643	missense	probably benign	0.12
R4624:Pcdh9	UTSW	14	93886409	missense	probably damaging	1.00
R4712:Pcdh9	UTSW	14	93888631	missense	probably damaging	1.00
R4788:Pcdh9	UTSW	14	93887415	missense	probably damaging	1.00
R4831:Pcdh9	UTSW	14	93887941	missense	probably damaging	1.00
R4883:Pcdh9	UTSW	14	93888728	missense	possibly damaging	0.83
R5034:Pcdh9	UTSW	14	93326849	missense	probably benign	0.13
R5175:Pcdh9	UTSW	14	93888443	missense	probably damaging	1.00
R5637:Pcdh9	UTSW	14	93885762	missense	possibly damaging	0.91
R5743:Pcdh9	UTSW	14	93886724	missense	probably damaging	1.00
R5753:Pcdh9	UTSW	14	93888161	missense	probably damaging	1.00
R5770:Pcdh9	UTSW	14	93886943	missense	probably damaging	1.00
R5900:Pcdh9	UTSW	14	93326720	missense	probably damaging	0.98
R5986:Pcdh9	UTSW	14	93887048	missense	probably damaging	1.00
R6052:Pcdh9	UTSW	14	93885846	missense	probably benign	0.40
R6113:Pcdh9	UTSW	14	93887108	missense	probably damaging	1.00
R6223:Pcdh9	UTSW	14	93015733	missense	probably benign	0.18
R6415:Pcdh9	UTSW	14	93015842	missense	possibly damaging	0.83
R6435:Pcdh9	UTSW	14	93887844	missense	probably benign	0.01
R7064:Pcdh9	UTSW	14	93886149	missense	probably damaging	1.00
R7143:Pcdh9	UTSW	14	93888272	missense	probably damaging	0.99
R7219:Pcdh9	UTSW	14	93015780	missense	possibly damaging	0.87
R7262:Pcdh9	UTSW	14	93015705	missense	probably benign	0.01
R7354:Pcdh9	UTSW	14	93888270	missense	probably benign	0.28
R7369:Pcdh9	UTSW	14	93886367	missense	possibly damaging	0.67
R7427:Pcdh9	UTSW	14	93887111	missense	probably damaging	1.00
R7428:Pcdh9	UTSW	14	93887111	missense	probably damaging	1.00
R7780:Pcdh9	UTSW	14	93886551	missense	possibly damaging	0.91
R7870:Pcdh9	UTSW	14	93887257	missense	probably damaging	0.97
R7921:Pcdh9	UTSW	14	93015565	missense	probably benign
R8052:Pcdh9	UTSW	14	93885786	missense	probably benign	0.00
R8252:Pcdh9	UTSW	14	93888650	missense	probably damaging	1.00
R8671:Pcdh9	UTSW	14	93888650	missense	probably damaging	1.00
R8672:Pcdh9	UTSW	14	93887093	missense	probably benign	0.08
R8724:Pcdh9	UTSW	14	93887147	missense	probably benign	0.19
R8974:Pcdh9	UTSW	14	93887677	missense	probably benign	0.20
R9044:Pcdh9	UTSW	14	93886811	missense	probably damaging	1.00
X0012:Pcdh9	UTSW	14	93886644	missense	possibly damaging	0.71
X0067:Pcdh9	UTSW	14	93326849	missense	probably benign	0.13

Predicted Primers

PCR Primer
(F):5'- CACTCTGAGGCACTGAAGTGATCTG -3'
(R):5'- GAAGAGAAGCCAGCACCTACTGATG -3'

Sequencing Primer
(F):5'- TCATGAACGGCATCATCGG -3'
(R):5'- CTTGTGGTCAACATAAGTGACCTG -3'

Posted On

2013-06-12