Mutagenetix > Incidental Mutations

Incidental Mutation 'R8974:Pcdh9'

683333

Institutional Source

Beutler Lab

Gene Symbol

Pcdh9

Ensembl Gene

ENSMUSG00000055421

Gene Name

protocadherin 9

Synonyms

C630029H24Rik, A730003J17Rik, C530050I23Rik, LOC382930, 1500001L12Rik

Accession Numbers

Is this an essential gene?

Probably non essential (E-score: 0.199) question?

Stock #

R8974 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

93013410-93890679 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

A to C at 93887677 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Asparagine to Lysine at position 352 (N352K)

Ref Sequence

ENSEMBL: ENSMUSP00000070935 (fasta)

Gene Model

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

AlphaFold

F8VPK8

Predicted Effect

probably benign
Transcript: ENSMUST00000068992
AA Change: N352K

PolyPhen 2 Score 0.196 (Sensitivity: 0.92; Specificity: 0.87)

SMART Domains

Protein: ENSMUSP00000070935
Gene: ENSMUSG00000055421
AA Change: N352K

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: N229K

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

SMART Domains

Protein: ENSMUSP00000142260
Gene: ENSMUSG00000055421
AA Change: N229K

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

probably damaging
Transcript: ENSMUST00000193901
AA Change: N352K

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

SMART Domains

Protein: ENSMUSP00000141759
Gene: ENSMUSG00000055421
AA Change: N352K

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 benign
Transcript: ENSMUST00000194056
AA Change: N352K

PolyPhen 2 Score 0.196 (Sensitivity: 0.92; Specificity: 0.87)

SMART Domains

Protein: ENSMUSP00000141602
Gene: ENSMUSG00000055421
AA Change: N352K

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: N352K

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

SMART Domains

Protein: ENSMUSP00000142224
Gene: ENSMUSG00000055421
AA Change: N352K

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 benign
Transcript: ENSMUST00000195826
AA Change: N352K

PolyPhen 2 Score 0.196 (Sensitivity: 0.92; Specificity: 0.87)

SMART Domains

Protein: ENSMUSP00000141396
Gene: ENSMUSG00000055421
AA Change: N352K

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

0.5967

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.7%
20x: 99.0%

Validation Efficiency

100% (59/59)

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: 60 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Acat3	A	G	17: 12,924,829	V342A	probably damaging	Het
Acot4	T	C	12: 84,043,741	F404S	probably benign	Het
Alpk1	T	C	3: 127,679,931	T808A	probably benign	Het
Apba3	T	C	10: 81,273,198	V154A		Het
Arhgap27	A	T	11: 103,333,930	F476I	possibly damaging	Het
Asah2	A	T	19: 32,052,905	D122E	probably benign	Het
Asb10	T	C	5: 24,540,211	I47V	probably benign	Het
Catsperd	A	G	17: 56,652,525	T322A	possibly damaging	Het
Ccdc142	T	C	6: 83,101,982	V100A	probably benign	Het
Cdc5l	A	T	17: 45,404,695	C664S	possibly damaging	Het
Cep250	C	T	2: 155,970,122	A446V	unknown	Het
Cep89	A	G	7: 35,398,068	S40G	probably damaging	Het
Csmd2	A	G	4: 128,552,587	K3315R		Het
Cyp2d34	T	C	15: 82,616,336	E434G	probably damaging	Het
Degs1	A	G	1: 182,279,713	Y30H	probably benign	Het
Eps8l1	A	G	7: 4,471,818	D266G	probably damaging	Het
Fam168a	A	T	7: 100,835,404	T234S	probably benign	Het
Fzd3	G	T	14: 65,234,991	Q443K	possibly damaging	Het
Galnt7	A	G	8: 57,652,900	S27P		Het
Gm20767	T	A	13: 120,154,950	D108E	probably benign	Het
Gm30302	T	C	13: 49,786,080	D718G	probably benign	Het
Gpr162	T	C	6: 124,860,913	D258G	probably damaging	Het
Hdac2	A	G	10: 36,986,344	Y68C	probably damaging	Het
Lmbr1l	A	G	15: 98,912,527	C68R	probably damaging	Het
Loxhd1	A	G	18: 77,431,203	T1902A	possibly damaging	Het
Lrrc4c	T	C	2: 97,629,647	M206T	probably damaging	Het
Lrrc75b	T	C	10: 75,554,014	T168A	probably benign	Het
Magi1	A	G	6: 93,697,242	F1003L	probably damaging	Het
Map1s	T	C	8: 70,914,350	L633P	probably damaging	Het
Mapk11	G	A	15: 89,143,811	T341I	probably benign	Het
Mycbp2	A	T	14: 103,124,421	V4441D	probably damaging	Het
Nin	T	C	12: 70,078,158	E130G		Het
Nod2	T	A	8: 88,663,805	Y247N	probably damaging	Het
Nudcd3	A	T	11: 6,193,163	V169E	probably benign	Het
Olfr1364	A	T	13: 21,574,033	I141N	probably damaging	Het
Olfr621-ps1	T	C	7: 103,629,282	Y226C	unknown	Het
Olfr764-ps1	A	C	10: 129,034,036	C269G	probably damaging	Het
Pfpl	G	A	19: 12,428,475	G30D	probably damaging	Het
Pi15	A	G	1: 17,621,451	D159G	possibly damaging	Het
Plxna4	G	T	6: 32,239,512	R543S	possibly damaging	Het
Ppp1r12c	C	T	7: 4,483,699	E543K	probably damaging	Het
Prkdc	T	A	16: 15,799,862		probably benign	Het
Proca1	T	C	11: 78,205,318	S172P	probably damaging	Het
Ralgapa1	C	A	12: 55,677,006	M1578I	probably benign	Het
Rnf103	C	A	6: 71,509,108	A241E	probably damaging	Het
Rorb	T	C	19: 18,977,706	D182G	probably benign	Het
Ryr3	T	C	2: 112,912,279	K485E	possibly damaging	Het
Sec24d	G	A	3: 123,305,849	D324N	probably damaging	Het
Serpina3f	T	A	12: 104,217,383	I168N	probably damaging	Het
Sidt1	A	T	16: 44,281,617	*62R	probably null	Het
Slc22a27	A	C	19: 7,926,386	S129A	probably damaging	Het
Stab1	A	G	14: 31,160,822	V408A	probably benign	Het
Svil	G	T	18: 5,099,650	G1729W	probably damaging	Het
Tbx20	A	G	9: 24,769,786	S137P	probably damaging	Het
Trem2	G	A	17: 48,348,571	R52Q	probably damaging	Het
Trim55	T	C	3: 19,645,439	S112P	probably damaging	Het
Vmn1r172	A	T	7: 23,660,415	M242L	probably benign	Het
Vmn2r91	G	A	17: 18,105,374	A85T	probably benign	Het
Zc3h3	T	C	15: 75,785,603	T580A	probably benign	Het
Zfp451	A	G	1: 33,777,454	C472R	probably damaging	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
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
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'- CACTGCCTTCAAATGAAATGGG -3'
(R):5'- TGCAGACATAGGCAGTAATGC -3'

Sequencing Primer
(F):5'- TGCCTTCAAATGAAATGGGACCTC -3'
(R):5'- AAATCCGGTATATTTTTGGTGCCCAG -3'

Posted On

2021-10-11