Mutagenetix > Incidental Mutation

Incidental Mutation 'R4825:Pcdh1'

371472

Institutional Source

Beutler Lab

Gene Symbol

Pcdh1

Ensembl Gene

ENSMUSG00000051375

Gene Name

protocadherin 1

Synonyms

2010005A06Rik

MMRRC Submission

042441-MU

Accession Numbers

Essential gene?

Possibly non essential (E-score: 0.345) question?

Stock #

R4825 (G1)

Quality Score

224

Status

Not validated

Chromosome

Chromosomal Location

38185914-38212053 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 38189859 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Methionine to Valine at position 974 (M974V)

Ref Sequence

ENSEMBL: ENSMUSP00000125576 (fasta)

Gene Model

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

AlphaFold

Q8CFX3

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

possibly damaging
Transcript: ENSMUST00000161701
AA Change: M974V

PolyPhen 2 Score 0.767 (Sensitivity: 0.85; Specificity: 0.92)

SMART Domains

Protein: ENSMUSP00000125576
Gene: ENSMUSG00000051375
AA Change: M974V

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

Coding Region Coverage

1x: 99.1%
3x: 98.4%
10x: 96.8%
20x: 93.8%

Validation Efficiency

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: 130 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1700012B07Rik	C	A	11: 109,791,672	L229F	probably benign	Het
A930002H24Rik	A	C	17: 63,863,608	S62A	unknown	Het
Abca12	T	A	1: 71,302,685	Q1039L	possibly damaging	Het
Adgrg5	T	A	8: 94,941,734	F476I	possibly damaging	Het
AI314180	G	A	4: 58,850,911	L421F	probably damaging	Het
Alms1	A	G	6: 85,678,245	K2789E	probably damaging	Het
Arrdc2	G	A	8: 70,839,277		probably null	Het
Atp2b1	T	A	10: 99,009,564	I743K	probably damaging	Het
Atp6v1c2	C	T	12: 17,289,060	G230D	probably benign	Het
AU040320	G	A	4: 126,791,793	C54Y	probably damaging	Het
BC024139	C	T	15: 76,120,317	V680I	possibly damaging	Het
Bckdhb	A	G	9: 83,988,905	D156G	probably damaging	Het
Canx	T	A	11: 50,308,809	D143V	probably benign	Het
Ccdc180	T	A	4: 45,912,794	V591E	possibly damaging	Het
Ccno	T	C	13: 112,988,099	S68P	probably benign	Het
Cdc45	C	T	16: 18,784,863	E527K	probably damaging	Het
Cep290	T	A	10: 100,488,348	D14E	probably damaging	Het
Cgnl1	A	G	9: 71,630,524	V1238A	probably benign	Het
Ciz1	C	T	2: 32,371,741	A455V	probably damaging	Het
Coro2b	T	A	9: 62,454,623	Y86F	probably benign	Het
Csf2ra	C	T	19: 61,226,552	R158Q	probably benign	Het
Cubn	A	T	2: 13,325,225	I2615N	probably damaging	Het
Dhx8	C	T	11: 101,738,170	R129*	probably null	Het
Disc1	T	A	8: 125,135,302	M471K	possibly damaging	Het
Dmxl2	G	T	9: 54,404,041	L1799I	probably benign	Het
Dnah2	A	G	11: 69,423,205	S4108P	probably damaging	Het
Ehmt2	C	G	17: 34,906,964	P211R	probably benign	Het
Eif4g3	A	G	4: 138,194,081	D1557G	probably benign	Het
Epha5	T	C	5: 84,233,840	D384G	probably damaging	Het
Etl4	A	G	2: 20,806,927	I1274V	probably damaging	Het
Fam160a1	G	A	3: 85,673,432	P489S	possibly damaging	Het
Fip1l1	G	A	5: 74,588,205		probably null	Het
Fubp1	T	C	3: 152,217,890		probably null	Het
Glul	T	C	1: 153,903,044	V33A	probably benign	Het
Gm4846	A	G	1: 166,491,668	F167S	probably damaging	Het
Heatr6	T	A	11: 83,758,322	L168M	probably damaging	Het
Hif1a	T	A	12: 73,932,401	I233N	probably damaging	Het
Hivep2	T	A	10: 14,131,319	H1220Q	possibly damaging	Het
Igkv8-21	T	C	6: 70,315,426	I9M	probably benign	Het
Izumo1	T	A	7: 45,624,987	C62*	probably null	Het
Jakmip3	G	A	7: 139,026,766	E424K	probably damaging	Het
Klhl2	A	G	8: 64,752,813	V358A	probably damaging	Het
Klk10	C	G	7: 43,783,598	D139E	probably damaging	Het
Klk14	T	C	7: 43,692,076	C51R	probably damaging	Het
Klk5	T	G	7: 43,845,390	I99S	probably damaging	Het
L3hypdh	T	C	12: 72,077,393	T258A	probably benign	Het
Lrp5	A	G	19: 3,614,292	Y812H	probably damaging	Het
Lrrc40	T	A	3: 158,061,330	L474*	probably null	Het
Mkks	A	T	2: 136,880,655	M194K	probably benign	Het
Mmp20	A	G	9: 7,654,120	D347G	probably damaging	Het
Mmp27	A	G	9: 7,581,194	E460G	probably damaging	Het
Mms22l	T	C	4: 24,536,226	F605S	probably damaging	Het
Mpzl3	A	G	9: 45,068,329	S193G	probably benign	Het
Muc4	A	T	16: 32,751,747	T542S	probably benign	Het
Muc5b	T	C	7: 141,868,465	L4446P	possibly damaging	Het
Mxi1	C	A	19: 53,370,338	S131*	probably null	Het
Nanog	G	T	6: 122,713,340	A210S	probably benign	Het
Nrcam	C	T	12: 44,575,986	Q988*	probably null	Het
Nsg1	C	A	5: 38,159,047		probably benign	Het
Ogfod3	G	A	11: 121,195,201	A189V	probably benign	Het
Olfr1121	T	A	2: 87,372,088	C185*	probably null	Het
Olfr1228	T	C	2: 89,248,690		probably null	Het
Olfr1240	A	G	2: 89,439,865	V138A	probably benign	Het
Olfr1260	G	A	2: 89,978,153	C125Y	probably damaging	Het
Olfr1465	A	T	19: 13,314,320		probably null	Het
Olfr548-ps1	T	A	7: 102,542,380	V148E	possibly damaging	Het
Olfr58	T	G	9: 19,783,576	S148A	possibly damaging	Het
Olfr632	T	C	7: 103,937,503	V41A	probably benign	Het
Olfr920	A	T	9: 38,756,407	T240S	probably damaging	Het
Olfr980	A	T	9: 40,006,742	M69K	possibly damaging	Het
Orc3	A	T	4: 34,571,774	M665K	possibly damaging	Het
Pabpc1	A	G	15: 36,597,011	S591P	probably damaging	Het
Parp6	T	A	9: 59,624,362		probably null	Het
Pcdhb22	T	A	18: 37,520,660	V727E	possibly damaging	Het
Pex5l	T	C	3: 32,992,985	E272G	probably damaging	Het
Pglyrp2	G	T	17: 32,418,261	N264K	probably benign	Het
Phxr4	T	A	9: 13,431,586		probably benign	Het
Piezo2	A	G	18: 63,144,954	F293S	probably damaging	Het
Pkhd1	T	C	1: 20,537,401	D1077G	probably damaging	Het
Plekhs1	A	G	19: 56,473,268		probably null	Het
Prex1	G	T	2: 166,585,857	C788*	probably null	Het
Prrt3	A	T	6: 113,498,138	M41K	probably benign	Het
Ptgir	T	C	7: 16,908,843	V326A	probably damaging	Het
Ptprg	T	A	14: 12,220,654	D455E	probably damaging	Het
Ptpru	T	A	4: 131,799,603	Q686L	probably benign	Het
Pxdc1	G	T	13: 34,630,360	T190K	probably benign	Het
Rap1b	A	T	10: 117,818,582	C118S	probably benign	Het
Rapgef2	T	C	3: 79,083,227	M915V	probably benign	Het
Rnd2	C	T	11: 101,468,999	L57F	probably damaging	Het
Rpe65	C	T	3: 159,624,681	A495V	probably benign	Het
Samd15	A	G	12: 87,200,834	T98A	possibly damaging	Het
Sdk1	T	G	5: 141,582,294	D82E	probably benign	Het
Slc26a7	T	C	4: 14,546,309	D340G	probably benign	Het
Slc6a15	T	A	10: 103,418,060	M619K	probably benign	Het
Slc7a4	C	A	16: 17,574,521	D350Y	probably damaging	Het
Slk	T	G	19: 47,619,956	N449K	probably benign	Het
Spta1	A	T	1: 174,244,042		probably null	Het
Sptbn5	A	T	2: 120,055,893		probably benign	Het
Srd5a2	A	T	17: 74,047,805	V8D	probably benign	Het
Srgap3	G	A	6: 112,727,310	A906V	probably benign	Het
Stab2	A	T	10: 86,947,147	M679K	probably benign	Het
Stk3	T	C	15: 34,999,908	I291V	probably benign	Het
Supt6	T	A	11: 78,208,134	Q1637L	possibly damaging	Het
Svil	T	C	18: 5,114,564	F2047S	probably damaging	Het
Swsap1	A	G	9: 21,955,988	E76G	probably benign	Het
Syndig1	G	T	2: 149,899,553	G20C	probably damaging	Het
Synj2bp	A	T	12: 81,502,152	N104K	probably damaging	Het
Synpo2	T	A	3: 123,114,419	D416V	probably damaging	Het
Tacc3	G	T	5: 33,672,013	C620F	probably damaging	Het
Tanc1	A	G	2: 59,699,422	E19G	probably damaging	Het
Tarsl2	C	T	7: 65,647,554	A139V	probably benign	Het
Tbc1d22a	T	A	15: 86,351,734	C365S	probably damaging	Het
Tdpoz2	T	C	3: 93,652,074	H197R	possibly damaging	Het
Tha1	A	T	11: 117,869,379	N300K	probably damaging	Het
Tm6sf1	T	A	7: 81,865,260	F70L	probably damaging	Het
Tmem132b	T	A	5: 125,783,433	S581T	probably benign	Het
Tmem206	A	T	1: 191,340,843	I154F	probably damaging	Het
Tnfsf13	G	T	11: 69,685,249	S4*	probably null	Het
Tonsl	G	A	15: 76,633,248	S757L	probably benign	Het
Trem2	G	T	17: 48,351,691	R161S	possibly damaging	Het
Trpm2	A	T	10: 77,941,173	V430E	probably damaging	Het
Ttc14	T	A	3: 33,801,369	D154E	possibly damaging	Het
Ugt2b37	T	C	5: 87,250,639	M313V	possibly damaging	Het
Uhrf1bp1	G	A	17: 27,877,394	A107T	probably damaging	Het
Vmn2r24	A	G	6: 123,815,780	I689V	probably benign	Het
Wdr76	A	G	2: 121,542,494	T601A	probably benign	Het
Xirp1	T	C	9: 120,017,003	D938G	possibly damaging	Het
Zfp608	A	T	18: 54,897,969	D966E	probably benign	Het
Zfp957	A	G	14: 79,214,356	M1T	probably null	Het
Zkscan16	A	T	4: 58,957,809	H697L	possibly 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
R0542:Pcdh1	UTSW	18	38189922	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
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
R8675:Pcdh1	UTSW	18	38199176	missense	probably damaging	1.00
R8851:Pcdh1	UTSW	18	38192102	missense	probably damaging	1.00
R8947:Pcdh1	UTSW	18	38199020	missense	possibly damaging	0.89
R9443:Pcdh1	UTSW	18	38197580	missense	probably damaging	1.00
R9448:Pcdh1	UTSW	18	38197439	missense	probably damaging	1.00
R9608:Pcdh1	UTSW	18	38197851	missense	possibly damaging	0.91
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'- AAGGGAATTTCCTCCAAGGTGG -3'
(R):5'- GTCAGAAGCAGAATGTGTATGC -3'

Sequencing Primer
(F):5'- TCCTTGCAGGAGTCATGGCTAC -3'
(R):5'- TGTGTATGCTAAGGAGAGGCC -3'

Posted On

2016-03-01