Mutagenetix > Incidental Mutations

Incidental Mutation 'R1988:Pcdh9'

222904

Institutional Source

Beutler Lab

Gene Symbol

Pcdh9

Ensembl Gene

ENSMUSG00000055421

Gene Name

protocadherin 9

Synonyms

C630029H24Rik, A730003J17Rik, C530050I23Rik, LOC382930, 1500001L12Rik

MMRRC Submission

040000-MU

Accession Numbers

Is this an essential gene?

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

Stock #

R1988 (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 93888305 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Proline to Leucine at position 143 (P143L)

Ref Sequence

ENSEMBL: ENSMUSP00000141759 (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: P143L

PolyPhen 2 Score 0.994 (Sensitivity: 0.69; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000070935
Gene: ENSMUSG00000055421
AA Change: P143L

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: P20L

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

SMART Domains

Protein: ENSMUSP00000142260
Gene: ENSMUSG00000055421
AA Change: P20L

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: P143L

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

SMART Domains

Protein: ENSMUSP00000141759
Gene: ENSMUSG00000055421
AA Change: P143L

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: P143L

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000141602
Gene: ENSMUSG00000055421
AA Change: P143L

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 benign
Transcript: ENSMUST00000195376
AA Change: P143L

PolyPhen 2 Score 0.109 (Sensitivity: 0.93; Specificity: 0.86)

SMART Domains

Protein: ENSMUSP00000142224
Gene: ENSMUSG00000055421
AA Change: P143L

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: P143L

PolyPhen 2 Score 0.994 (Sensitivity: 0.69; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000141396
Gene: ENSMUSG00000055421
AA Change: P143L

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

0.1364

Coding Region Coverage

1x: 99.2%
3x: 98.4%
10x: 96.6%
20x: 93.1%

Validation Efficiency

96% (79/82)

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: 77 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1700034J05Rik	T	A	6: 146,952,896	D216V	possibly damaging	Het
2610021A01Rik	C	T	7: 41,626,657	R595*	probably null	Het
Adgrl3	A	G	5: 81,688,567	D724G	probably damaging	Het
Akap6	T	C	12: 53,140,795	F1664S	possibly damaging	Het
Akt1	T	C	12: 112,655,151	I404V	probably benign	Het
Anxa13	T	A	15: 58,341,948		noncoding transcript	Het
Atoh1	T	C	6: 64,729,633	V104A	probably benign	Het
Brwd1	T	C	16: 96,021,237	D1256G	probably damaging	Het
C9	ATTTT	ATTT	15: 6,483,138		probably null	Het
Cd164	A	G	10: 41,523,181	T89A	probably benign	Het
Cep350	G	C	1: 155,933,104	N575K	possibly damaging	Het
Chrm5	A	G	2: 112,480,252	V173A	probably damaging	Het
Cnot1	A	G	8: 95,741,944	V1417A	possibly damaging	Het
Cntnap3	T	C	13: 64,758,390	T801A	probably damaging	Het
Cntnap5b	A	C	1: 100,072,140	K208Q	possibly damaging	Het
Crx	A	T	7: 15,869,347	V107D	possibly damaging	Het
Csrnp2	A	G	15: 100,489,440	F49S	probably damaging	Het
Ctbp1	A	G	5: 33,250,904	L228P	possibly damaging	Het
Ctdp1	A	T	18: 80,449,401	D626E	possibly damaging	Het
Cyp1a2	T	C	9: 57,682,286	T82A	possibly damaging	Het
Dnah3	T	A	7: 119,967,570	T2478S	possibly damaging	Het
Dnah3	T	G	7: 119,967,959	D2348A	probably damaging	Het
Dnah5	T	C	15: 28,343,591	I2379T	probably damaging	Het
Dnah6	A	G	6: 73,092,192	I2504T	probably damaging	Het
Dnase1l2	A	C	17: 24,441,651	W138G	probably damaging	Het
Dopey2	T	A	16: 93,766,173	I855N	probably damaging	Het
Dsc3	T	A	18: 19,965,846	N759Y	possibly damaging	Het
Dtx2	C	T	5: 136,032,293	R510*	probably null	Het
Fat4	G	T	3: 38,887,115	M52I	probably benign	Het
Fat4	G	A	3: 38,996,090	E4034K	probably damaging	Het
Fezf2	T	C	14: 12,344,350	K279R	probably damaging	Het
Fsip2	G	T	2: 82,976,517	W1060L	possibly damaging	Het
G6pc	T	A	11: 101,367,942	I49N	probably damaging	Het
Gars	A	G	6: 55,077,772	E688G	probably null	Het
Gdf11	T	C	10: 128,885,242	N361S	probably benign	Het
Gli3	A	C	13: 15,726,380	M1451L	probably benign	Het
Heatr3	T	C	8: 88,150,317	I329T	probably benign	Het
Herc3	T	G	6: 58,884,975		probably null	Het
Hrnr	A	G	3: 93,332,604	N3383S	unknown	Het
Igsf3	A	T	3: 101,431,296	I309F	probably benign	Het
Kif21b	C	T	1: 136,152,264	R513W	probably damaging	Het
Kif7	G	T	7: 79,699,241	H1195Q	probably benign	Het
Lpcat4	T	C	2: 112,242,542	V182A	possibly damaging	Het
Map3k21	T	A	8: 125,927,555	I371N	probably benign	Het
Mns1	G	A	9: 72,448,759		probably null	Het
Myo3a	A	G	2: 22,578,128	T465A	possibly damaging	Het
Nlrc4	A	T	17: 74,426,943	S992T	probably benign	Het
Notch4	G	A	17: 34,587,588	G1833E	possibly damaging	Het
Olfr160	A	T	9: 37,711,697	I194K	possibly damaging	Het
Olfr467	A	T	7: 107,814,700	I39L	probably benign	Het
Olfr600	T	A	7: 103,346,109	Y273F	possibly damaging	Het
Olfr666	T	C	7: 104,892,903	T242A	probably damaging	Het
Olfr998	G	A	2: 85,590,641	V34I	probably benign	Het
Pik3cd	T	A	4: 149,663,203	T28S	probably damaging	Het
Pkd1	G	T	17: 24,576,592		probably null	Het
Plk4	A	T	3: 40,805,817	S383C	possibly damaging	Het
Plxna2	T	C	1: 194,643,989	L77P	probably damaging	Het
Ppm1f	T	C	16: 16,923,666	S335P	probably damaging	Het
Prr16	C	T	18: 51,303,277	P276L	probably damaging	Het
Rilp	A	G	11: 75,510,933		probably null	Het
Rspry1	A	G	8: 94,632,054		probably null	Het
Serpinb9b	T	C	13: 33,029,559	V33A	probably benign	Het
Slc4a10	C	A	2: 62,268,204	Q561K	probably damaging	Het
Smyd5	T	C	6: 85,438,136	I42T	possibly damaging	Het
Stk17b	T	C	1: 53,761,082	N246D	probably damaging	Het
Suco	T	C	1: 161,818,811		probably null	Het
Tcrg-C3	C	A	13: 19,260,994	F37L	probably damaging	Het
Tecpr1	C	T	5: 144,204,697	V785M	possibly damaging	Het
Telo2	C	T	17: 25,101,668	V756I	probably benign	Het
Tgm1	C	T	14: 55,705,577	R602H	probably benign	Het
Timeless	A	G	10: 128,244,187	T402A	probably damaging	Het
Tnfaip2	T	A	12: 111,449,891		probably null	Het
Trim5	A	G	7: 104,265,621	S414P	probably damaging	Het
Txnip	A	G	3: 96,559,750	T247A	possibly damaging	Het
Vmn1r174	A	T	7: 23,754,625	T239S	probably damaging	Het
Vmn1r231	T	A	17: 20,889,950	E234D	probably damaging	Het
Zranb3	A	T	1: 127,959,743	N982K	probably benign	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
R0499:Pcdh9	UTSW	14	93886235	missense	probably damaging	1.00
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
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'- GCTGAACAATCAATTGCGGC -3'
(R):5'- CCTCTGGTGAAAGTATCGAGTAGC -3'

Sequencing Primer
(F):5'- GAACAATCAATTGCGGCCACTTTTC -3'
(R):5'- ACTGGGGAGATTTTCACAACCTC -3'

Posted On

2014-08-25