Mutagenetix > Incidental Mutations

Incidental Mutation 'R0542:Pcdh1'

50015

Institutional Source

Beutler Lab

Gene Symbol

Pcdh1

Ensembl Gene

ENSMUSG00000051375

Gene Name

protocadherin 1

Synonyms

2010005A06Rik

MMRRC Submission

038734-MU

Accession Numbers

Is this an essential gene?

Possibly non essential (E-score: 0.342) question?

Stock #

R0542 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

38185914-38212053 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

C to T at 38189922 bp

Zygosity

Heterozygous

Amino Acid Change

Valine to Isoleucine at position 953 (V953I)

Ref Sequence

ENSEMBL: ENSMUSP00000125576 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000160721] [ENSMUST00000161701]

Predicted Effect

probably benign
Transcript: ENSMUST00000160721

SMART Domains

Protein: ENSMUSP00000124732
Gene: ENSMUSG00000051375

Domain	Start	End	E-Value	Type
signal peptide	1	33	N/A	INTRINSIC
Pfam:Cadherin_2	36	120	9.9e-10	PFAM
CA	168	256	5.18e-18	SMART
low complexity region	310	321	N/A	INTRINSIC

Predicted Effect

probably damaging
Transcript: ENSMUST00000161701
AA Change: V953I

PolyPhen 2 Score 0.988 (Sensitivity: 0.73; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000125576
Gene: ENSMUSG00000051375
AA Change: V953I

Domain	Start	End	E-Value	Type
CA	29	117	5.18e-18	SMART
CA	141	224	5.68e-24	SMART
CA	256	343	1.84e-23	SMART
CA	367	449	2.99e-32	SMART
CA	473	552	9.36e-25	SMART
CA	578	659	9.9e-15	SMART
transmembrane domain	691	713	N/A	INTRINSIC
low complexity region	737	764	N/A	INTRINSIC
low complexity region	812	825	N/A	INTRINSIC
low complexity region	903	914	N/A	INTRINSIC
low complexity region	1029	1040	N/A	INTRINSIC
low complexity region	1059	1071	N/A	INTRINSIC

Meta Mutation Damage Score

0.1472

Coding Region Coverage

1x: 99.3%
3x: 98.6%
10x: 97.1%
20x: 95.0%

Validation Efficiency

99% (70/71)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene belongs to the protocadherin subfamily within the cadherin superfamily. The encoded protein is a membrane protein found at cell-cell boundaries. It is involved in neural cell adhesion, suggesting a possible role in neuronal development. The protein includes an extracelllular region, containing 7 cadherin-like domains, a transmembrane region and a C-terminal cytoplasmic region. Cells expressing the protein showed cell aggregation activity. Alternative splicing occurs in this gene. [provided by RefSeq, Jul 2008]

Allele List at MGI

Other mutations in this stock

Total: 69 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
8030411F24Rik	A	G	2: 148,782,172	N22S	probably benign	Het
Abhd12b	C	A	12: 70,163,495	N71K	possibly damaging	Het
Adgrl2	A	G	3: 148,859,218	I242T	probably damaging	Het
Adgrv1	A	G	13: 81,573,318	S714P	probably damaging	Het
Agap3	G	A	5: 24,500,186	R704Q	possibly damaging	Het
Ankrd11	T	C	8: 122,895,770	R448G	probably damaging	Het
Anks1b	T	C	10: 90,073,967		probably benign	Het
Caml	A	T	13: 55,623,161	Q24L	possibly damaging	Het
Cdc14b	G	A	13: 64,243,683	T124I	probably benign	Het
Clca2	A	G	3: 145,075,810		probably benign	Het
Col12a1	A	G	9: 79,605,328		probably null	Het
Crispld1	T	C	1: 17,746,768	V183A	possibly damaging	Het
Dhx40	C	T	11: 86,804,256		probably null	Het
Dmxl1	T	A	18: 49,893,694	D1956E	probably benign	Het
Dsc2	A	G	18: 20,051,226	V35A	probably damaging	Het
Dusp27	A	T	1: 166,101,284	M253K	possibly damaging	Het
Elovl2	A	G	13: 41,191,976		probably benign	Het
Gapvd1	T	C	2: 34,725,036		probably benign	Het
Gnaq	T	A	19: 16,219,618	I56N	probably damaging	Het
Gpr139	T	C	7: 119,145,083	D93G	probably benign	Het
Hars	C	T	18: 36,771,181	R215H	probably benign	Het
Helz2	C	A	2: 181,232,089	W2204L	probably damaging	Het
Itgb6	A	T	2: 60,605,136	C757S	possibly damaging	Het
Kpnb1	G	A	11: 97,187,572	T5I	probably benign	Het
Krt82	T	C	15: 101,545,600		probably benign	Het
Lgals9	T	A	11: 78,969,720	K175N	possibly damaging	Het
Lrp2	A	G	2: 69,428,654	I4564T	probably benign	Het
Mblac1	A	G	5: 138,194,536	T47A	possibly damaging	Het
Med12l	G	A	3: 59,042,401	D182N	probably damaging	Het
Megf9	A	G	4: 70,435,348	I407T	probably benign	Het
Mtmr6	A	T	14: 60,292,129		probably null	Het
Mtor	A	G	4: 148,540,450	T2173A	probably benign	Het
Mzt1	A	T	14: 99,040,502		probably benign	Het
Narf	T	C	11: 121,252,864	L444P	probably damaging	Het
Nsd1	A	T	13: 55,260,458	Q1305L	possibly damaging	Het
Ntsr1	A	G	2: 180,542,581	Y359C	probably damaging	Het
Olfm1	A	G	2: 28,214,628	D159G	possibly damaging	Het
Olfr168	A	T	16: 19,529,982	*313R	probably null	Het
Pcdhb11	A	T	18: 37,423,834	D739V	probably damaging	Het
Pdgfd	A	G	9: 6,359,769	N280S	probably damaging	Het
Per2	A	T	1: 91,438,332		probably null	Het
Pfkp	G	T	13: 6,621,992	C122*	probably null	Het
Plxna4	G	A	6: 32,192,297	R1322W	probably damaging	Het
Ppox	A	G	1: 171,279,244	L202P	probably damaging	Het
Ppp1r3e	G	A	14: 54,877,131	P58L	probably benign	Het
Prr23a2	A	C	9: 98,857,033	N148T	probably benign	Het
Psd	T	C	19: 46,314,210	T842A	probably damaging	Het
Ranbp2	C	T	10: 58,478,414	A1652V	probably benign	Het
Rragd	G	A	4: 33,007,103	V144M	probably damaging	Het
Sema6a	T	G	18: 47,248,576	D968A	probably damaging	Het
Slc30a5	A	T	13: 100,809,285		probably null	Het
Snx17	G	T	5: 31,196,551		probably null	Het
Syt14	G	T	1: 192,930,803	T563K	probably damaging	Het
Tada3	T	C	6: 113,375,214	K85E	probably damaging	Het
Tspear	T	C	10: 77,881,087	V532A	probably benign	Het
Ttc30b	A	G	2: 75,936,711	V566A	probably damaging	Het
Ttn	A	T	2: 76,893,109	C6426S	possibly damaging	Het
Unc79	T	C	12: 103,094,178		probably benign	Het
Usp19	A	G	9: 108,494,385		probably null	Het
Vav3	G	A	3: 109,527,430	D426N	probably damaging	Het
Vezt	T	C	10: 94,007,096		probably null	Het
Vldlr	G	T	19: 27,236,255	R114L	probably benign	Het
Wdr34	A	G	2: 30,031,825	V508A	probably damaging	Het
Wwc2	C	T	8: 47,868,379	V567I	unknown	Het
Zfp423	T	C	8: 87,780,609	T911A	probably damaging	Het
Zfp719	A	G	7: 43,589,253		probably null	Het
Zkscan16	A	T	4: 58,956,597	H293L	possibly damaging	Het
Zkscan6	A	C	11: 65,828,699	N515T	possibly damaging	Het
Znfx1	A	G	2: 167,055,655	S450P	probably damaging	Het

Other mutations in Pcdh1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00714:Pcdh1	APN	18	38198729	missense	possibly damaging	0.65
IGL00919:Pcdh1	APN	18	38202812	nonsense	probably null
IGL01744:Pcdh1	APN	18	38203249	missense	probably damaging	1.00
PIT4260001:Pcdh1	UTSW	18	38203366	missense	probably damaging	0.99
R1449:Pcdh1	UTSW	18	38189876	missense	probably damaging	0.99
R1540:Pcdh1	UTSW	18	38189726	missense	probably benign	0.01
R1642:Pcdh1	UTSW	18	38199230	missense	possibly damaging	0.84
R1672:Pcdh1	UTSW	18	38192180	missense	probably damaging	1.00
R1695:Pcdh1	UTSW	18	38202868	missense	probably damaging	1.00
R1727:Pcdh1	UTSW	18	38203032	nonsense	probably null
R1781:Pcdh1	UTSW	18	38189924	missense	probably damaging	1.00
R1793:Pcdh1	UTSW	18	38198885	missense	probably damaging	0.99
R1839:Pcdh1	UTSW	18	38199485	missense	possibly damaging	0.82
R1843:Pcdh1	UTSW	18	38192225	splice site	probably null
R1882:Pcdh1	UTSW	18	38202842	missense	possibly damaging	0.49
R2261:Pcdh1	UTSW	18	38198657	missense	probably benign	0.01
R2262:Pcdh1	UTSW	18	38198657	missense	probably benign	0.01
R2263:Pcdh1	UTSW	18	38198657	missense	probably benign	0.01
R2511:Pcdh1	UTSW	18	38199479	missense	possibly damaging	0.95
R2937:Pcdh1	UTSW	18	38189762	missense	probably benign	0.40
R3941:Pcdh1	UTSW	18	38199458	missense	probably benign	0.02
R3942:Pcdh1	UTSW	18	38199458	missense	probably benign	0.02
R4057:Pcdh1	UTSW	18	38198897	missense	probably damaging	0.98
R4155:Pcdh1	UTSW	18	38203106	missense	probably damaging	0.99
R4169:Pcdh1	UTSW	18	38198305	missense	probably damaging	1.00
R4617:Pcdh1	UTSW	18	38197860	missense	probably benign	0.00
R4690:Pcdh1	UTSW	18	38203475	missense	probably benign	0.33
R4825:Pcdh1	UTSW	18	38189859	missense	possibly damaging	0.77
R5201:Pcdh1	UTSW	18	38198918	missense	probably damaging	0.98
R5266:Pcdh1	UTSW	18	38192199	missense	probably damaging	1.00
R5267:Pcdh1	UTSW	18	38192199	missense	probably damaging	1.00
R5351:Pcdh1	UTSW	18	38197766	missense	probably damaging	1.00
R5568:Pcdh1	UTSW	18	38197367	missense	probably damaging	1.00
R5729:Pcdh1	UTSW	18	38202946	missense	probably damaging	1.00
R5731:Pcdh1	UTSW	18	38198598	missense	probably damaging	1.00
R6043:Pcdh1	UTSW	18	38203274	missense	probably damaging	0.97
R6278:Pcdh1	UTSW	18	38199210	missense	probably benign	0.29
R6333:Pcdh1	UTSW	18	38198807	missense	probably benign	0.25
R6498:Pcdh1	UTSW	18	38197437	missense	probably benign	0.18
R6937:Pcdh1	UTSW	18	38203475	missense	possibly damaging	0.86
R6994:Pcdh1	UTSW	18	38198500	missense	probably damaging	1.00
R7242:Pcdh1	UTSW	18	38203217	missense	probably benign	0.06
R7289:Pcdh1	UTSW	18	38189913	missense	probably damaging	0.99
R7391:Pcdh1	UTSW	18	38202785	missense	possibly damaging	0.95
R7702:Pcdh1	UTSW	18	38203516	missense	unknown
R7738:Pcdh1	UTSW	18	38197476	missense	probably benign	0.02
R7849:Pcdh1	UTSW	18	38189609	missense	probably benign	0.01
R7941:Pcdh1	UTSW	18	38199080	missense	probably damaging	1.00
R8109:Pcdh1	UTSW	18	38198996	missense	probably damaging	1.00
X0027:Pcdh1	UTSW	18	38189788	nonsense	probably null
Z1088:Pcdh1	UTSW	18	38198067	missense	probably damaging	1.00
Z1176:Pcdh1	UTSW	18	38198688	missense	possibly damaging	0.79

Predicted Primers

PCR Primer
(F):5'- TCACAGGTAGATCTCACGCTTGGC -3'
(R):5'- TCCTAGAGGGCAGCAGAATAGTGAC -3'

Sequencing Primer
(F):5'- CTACTGTGGGAGAAGGCACTG -3'
(R):5'- ATAGTGACAGCGGGCCAC -3'

Posted On

2013-06-12