Mutagenetix > Incidental Mutation

Incidental Mutation 'R1839:Pcdh1'

205651

Institutional Source

Beutler Lab

Gene Symbol

Pcdh1

Ensembl Gene

ENSMUSG00000051375

Gene Name

protocadherin 1

Synonyms

2010005A06Rik

MMRRC Submission

045015-MU

Accession Numbers

Essential gene?

Possibly non essential (E-score: 0.329) question?

Stock #

R1839 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

38185914-38212053 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 38199485 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Aspartic acid to Glycine at position 155 (D155G)

Ref Sequence

ENSEMBL: ENSMUSP00000125576 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000057185] [ENSMUST00000159405] [ENSMUST00000160721] [ENSMUST00000161701] [ENSMUST00000193828] [ENSMUST00000194312]

AlphaFold

Q8CFX3

Predicted Effect

possibly damaging
Transcript: ENSMUST00000057185
AA Change: D294G

PolyPhen 2 Score 0.820 (Sensitivity: 0.84; Specificity: 0.93)

SMART Domains

Protein: ENSMUSP00000055199
Gene: ENSMUSG00000051375
AA Change: D294G

Domain	Start	End	E-Value	Type
signal peptide	1	33	N/A	INTRINSIC
Pfam:Cadherin_2	36	120	2e-8	PFAM
CA	168	256	5.18e-18	SMART
CA	280	363	5.68e-24	SMART
CA	395	482	1.84e-23	SMART
CA	506	588	2.99e-32	SMART
CA	612	691	9.36e-25	SMART
CA	717	798	9.9e-15	SMART
transmembrane domain	830	852	N/A	INTRINSIC
low complexity region	876	903	N/A	INTRINSIC
low complexity region	951	964	N/A	INTRINSIC

Predicted Effect

possibly damaging
Transcript: ENSMUST00000159405
AA Change: D294G

PolyPhen 2 Score 0.820 (Sensitivity: 0.84; Specificity: 0.93)

SMART Domains

Protein: ENSMUSP00000125309
Gene: ENSMUSG00000051375
AA Change: D294G

Domain	Start	End	E-Value	Type
signal peptide	1	33	N/A	INTRINSIC
Pfam:Cadherin_2	36	120	2e-8	PFAM
CA	168	256	5.18e-18	SMART
CA	280	363	5.68e-24	SMART
CA	395	482	1.84e-23	SMART
CA	506	588	2.99e-32	SMART
CA	612	691	9.36e-25	SMART
CA	717	798	9.9e-15	SMART
transmembrane domain	830	852	N/A	INTRINSIC
low complexity region	876	903	N/A	INTRINSIC
low complexity region	951	964	N/A	INTRINSIC

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: D155G

PolyPhen 2 Score 0.821 (Sensitivity: 0.84; Specificity: 0.93)

SMART Domains

Protein: ENSMUSP00000125576
Gene: ENSMUSG00000051375
AA Change: D155G

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

Predicted Effect

probably benign
Transcript: ENSMUST00000193828

SMART Domains

Protein: ENSMUSP00000142328
Gene: ENSMUSG00000051375

Domain	Start	End	E-Value	Type
low complexity region	18	48	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000194312

Meta Mutation Damage Score

0.1795

Coding Region Coverage

1x: 97.4%
3x: 96.7%
10x: 94.7%
20x: 90.6%

Validation Efficiency

98% (90/92)

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: 84 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1700006A11Rik	T	C	3: 124,409,720 (GRCm38)	T403A	probably damaging	Het
Acat3	T	A	17: 12,928,606 (GRCm38)	R175*	probably null	Het
Adam1b	C	A	5: 121,501,041 (GRCm38)	C647F	probably damaging	Het
Adam28	T	C	14: 68,639,210 (GRCm38)	N197S	possibly damaging	Het
Adcy2	C	T	13: 68,689,261 (GRCm38)		probably null	Het
Adcy5	A	T	16: 35,248,940 (GRCm38)	N426I	probably damaging	Het
Adgre1	T	C	17: 57,441,299 (GRCm38)	S500P	probably benign	Het
Aloxe3	A	G	11: 69,130,085 (GRCm38)	Y212C	probably damaging	Het
Ap3d1	A	G	10: 80,727,108 (GRCm38)	S180P	probably damaging	Het
Arhgap20	C	T	9: 51,849,326 (GRCm38)	R790W	probably damaging	Het
Atp8b4	C	A	2: 126,361,782 (GRCm38)	A757S	possibly damaging	Het
Begain	G	A	12: 109,035,323 (GRCm38)		probably benign	Het
Ccdc141	T	C	2: 77,011,665 (GRCm38)	E1474G	probably benign	Het
Ccdc88b	A	G	19: 6,854,109 (GRCm38)		probably benign	Het
Ccnk	A	G	12: 108,195,074 (GRCm38)	T195A	probably damaging	Het
Cd55b	C	A	1: 130,414,105 (GRCm38)	C265F	probably damaging	Het
Celsr3	A	G	9: 108,829,906 (GRCm38)	H1196R	probably benign	Het
Cenpt	T	C	8: 105,849,014 (GRCm38)	S190G	possibly damaging	Het
Chd8	T	C	14: 52,204,883 (GRCm38)	S2077G	probably benign	Het
Col6a5	G	A	9: 105,864,833 (GRCm38)	H2296Y	probably benign	Het
Cxxc4	C	A	3: 134,240,653 (GRCm38)	H332N	probably damaging	Het
Cyp24a1	T	C	2: 170,496,741 (GRCm38)	I12V	probably benign	Het
Cyp3a57	T	A	5: 145,381,301 (GRCm38)	L364Q	probably damaging	Het
Ddi2	T	C	4: 141,713,526 (GRCm38)	I47V	probably benign	Het
Ddx5	A	T	11: 106,784,897 (GRCm38)	D322E	probably benign	Het
Dhx40	A	G	11: 86,789,297 (GRCm38)	C405R	possibly damaging	Het
Emc1	T	C	4: 139,360,485 (GRCm38)	F100S	probably damaging	Het
Exoc2	T	C	13: 30,906,497 (GRCm38)		probably benign	Het
Gm10110	A	T	14: 89,897,836 (GRCm38)		noncoding transcript	Het
Gm17332	T	C	11: 31,182,386 (GRCm38)	H26R	possibly damaging	Het
Gna12	T	C	5: 140,762,612 (GRCm38)	N183S	probably benign	Het
Gpx6	A	G	13: 21,312,327 (GRCm38)	N24D	probably benign	Het
Gsdma3	C	T	11: 98,629,858 (GRCm38)	A105V	probably benign	Het
Hsd3b5	T	C	3: 98,619,728 (GRCm38)	Y134C	probably benign	Het
Ifi213	T	C	1: 173,589,600 (GRCm38)	I415M	probably damaging	Het
Ints9	C	A	14: 65,016,530 (GRCm38)	P278T	probably damaging	Het
Krt79	C	T	15: 101,937,938 (GRCm38)	E192K	possibly damaging	Het
Lrrk2	A	G	15: 91,683,134 (GRCm38)	N132S	probably benign	Het
Ltn1	T	A	16: 87,416,264 (GRCm38)	K470*	probably null	Het
Magi2	A	T	5: 20,465,827 (GRCm38)	T163S	probably damaging	Het
Mcm9	A	G	10: 53,541,553 (GRCm38)	M18T	probably damaging	Het
Med12l	A	G	3: 59,068,319 (GRCm38)	T212A	probably benign	Het
Mfhas1	T	C	8: 35,590,858 (GRCm38)	L829P	possibly damaging	Het
Mgme1	T	A	2: 144,279,487 (GRCm38)	C288S	probably benign	Het
Muc4	G	C	16: 32,753,919 (GRCm38)	R1265P	probably benign	Het
Myh7	T	C	14: 54,973,180 (GRCm38)	N1725S	possibly damaging	Het
Nat6	G	A	9: 107,583,017 (GRCm38)	R37H	possibly damaging	Het
Nme4	A	T	17: 26,092,097 (GRCm38)	W165R	probably damaging	Het
Nup205	T	A	6: 35,219,714 (GRCm38)	D1128E	probably benign	Het
Olfr291	T	C	7: 84,856,548 (GRCm38)	Y60H	probably damaging	Het
Olfr330	A	T	11: 58,529,373 (GRCm38)	Y204*	probably null	Het
Pex12	A	T	11: 83,297,822 (GRCm38)	S116T	probably damaging	Het
Plekhh1	C	T	12: 79,078,957 (GRCm38)		probably benign	Het
Plekhh3	A	G	11: 101,163,600 (GRCm38)		probably benign	Het
Pnpt1	T	C	11: 29,154,342 (GRCm38)	M572T	possibly damaging	Het
Ppp1r12b	T	C	1: 134,837,981 (GRCm38)	R667G	probably benign	Het
Rbpms2	ACTGCTGCTGCTGCTGC	ACTGCTGCTGCTGCTGCTGC	9: 65,651,666 (GRCm38)		probably benign	Het
Rgs14	T	C	13: 55,382,838 (GRCm38)		probably benign	Het
Rhbdf2	A	T	11: 116,600,191 (GRCm38)	V645E	possibly damaging	Het
Robo3	A	G	9: 37,422,327 (GRCm38)	V696A	probably benign	Het
Sall1	A	G	8: 89,028,716 (GRCm38)	F1212L	possibly damaging	Het
Sdc4	T	C	2: 164,429,012 (GRCm38)	E109G	probably benign	Het
Serpind1	G	T	16: 17,342,992 (GRCm38)	R462L	probably damaging	Het
Smad9	CTTT	CTT	3: 54,789,179 (GRCm38)		probably benign	Het
Sstr4	C	A	2: 148,395,533 (GRCm38)	N21K	probably benign	Het
Tap1	C	T	17: 34,188,109 (GRCm38)	A77V	possibly damaging	Het
Thap4	T	C	1: 93,750,287 (GRCm38)	E259G	probably benign	Het
Thra	A	G	11: 98,756,143 (GRCm38)	N30S	probably benign	Het
Tmem207	A	T	16: 26,524,821 (GRCm38)	V27E	possibly damaging	Het
Top3a	A	G	11: 60,753,888 (GRCm38)	V305A	probably damaging	Het
Trim59	A	T	3: 69,037,638 (GRCm38)	I123K	probably damaging	Het
Ttn	T	C	2: 76,861,495 (GRCm38)		probably benign	Het
Ubac1	T	A	2: 26,007,738 (GRCm38)	E290V	possibly damaging	Het
Unc13b	T	C	4: 43,258,308 (GRCm38)		probably benign	Het
Uri1	A	T	7: 37,967,389 (GRCm38)	D206E	probably benign	Het
Utp4	A	G	8: 106,913,454 (GRCm38)	H465R	probably benign	Het
Uvssa	T	C	5: 33,389,752 (GRCm38)	S221P	probably benign	Het
Vmn1r39	T	C	6: 66,805,233 (GRCm38)		probably null	Het
Vps39	A	T	2: 120,325,397 (GRCm38)	L514H	probably damaging	Het
Vps72	G	A	3: 95,119,218 (GRCm38)	R158Q	possibly damaging	Het
Wdr59	T	C	8: 111,485,340 (GRCm38)	D366G	probably benign	Het
Zfp366	C	A	13: 99,228,492 (GRCm38)	Q54K	probably damaging	Het
Zfp523	T	A	17: 28,194,993 (GRCm38)	I34N	probably damaging	Het
Zfp974	G	A	7: 27,910,356 (GRCm38)	P648L	possibly damaging	Het

Other mutations in Pcdh1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00714:Pcdh1	APN	18	38,198,729 (GRCm38)	missense	possibly damaging	0.65
IGL00919:Pcdh1	APN	18	38,202,812 (GRCm38)	nonsense	probably null
IGL01744:Pcdh1	APN	18	38,203,249 (GRCm38)	missense	probably damaging	1.00
PIT4260001:Pcdh1	UTSW	18	38,203,366 (GRCm38)	missense	probably damaging	0.99
R0542:Pcdh1	UTSW	18	38,189,922 (GRCm38)	missense	probably damaging	0.99
R1449:Pcdh1	UTSW	18	38,189,876 (GRCm38)	missense	probably damaging	0.99
R1540:Pcdh1	UTSW	18	38,189,726 (GRCm38)	missense	probably benign	0.01
R1642:Pcdh1	UTSW	18	38,199,230 (GRCm38)	missense	possibly damaging	0.84
R1672:Pcdh1	UTSW	18	38,192,180 (GRCm38)	missense	probably damaging	1.00
R1695:Pcdh1	UTSW	18	38,202,868 (GRCm38)	missense	probably damaging	1.00
R1727:Pcdh1	UTSW	18	38,203,032 (GRCm38)	nonsense	probably null
R1781:Pcdh1	UTSW	18	38,189,924 (GRCm38)	missense	probably damaging	1.00
R1793:Pcdh1	UTSW	18	38,198,885 (GRCm38)	missense	probably damaging	0.99
R1843:Pcdh1	UTSW	18	38,192,225 (GRCm38)	splice site	probably null
R1882:Pcdh1	UTSW	18	38,202,842 (GRCm38)	missense	possibly damaging	0.49
R2261:Pcdh1	UTSW	18	38,198,657 (GRCm38)	missense	probably benign	0.01
R2262:Pcdh1	UTSW	18	38,198,657 (GRCm38)	missense	probably benign	0.01
R2263:Pcdh1	UTSW	18	38,198,657 (GRCm38)	missense	probably benign	0.01
R2511:Pcdh1	UTSW	18	38,199,479 (GRCm38)	missense	possibly damaging	0.95
R2937:Pcdh1	UTSW	18	38,189,762 (GRCm38)	missense	probably benign	0.40
R3941:Pcdh1	UTSW	18	38,199,458 (GRCm38)	missense	probably benign	0.02
R3942:Pcdh1	UTSW	18	38,199,458 (GRCm38)	missense	probably benign	0.02
R4057:Pcdh1	UTSW	18	38,198,897 (GRCm38)	missense	probably damaging	0.98
R4155:Pcdh1	UTSW	18	38,203,106 (GRCm38)	missense	probably damaging	0.99
R4169:Pcdh1	UTSW	18	38,198,305 (GRCm38)	missense	probably damaging	1.00
R4617:Pcdh1	UTSW	18	38,197,860 (GRCm38)	missense	probably benign	0.00
R4690:Pcdh1	UTSW	18	38,203,475 (GRCm38)	missense	probably benign	0.33
R4825:Pcdh1	UTSW	18	38,189,859 (GRCm38)	missense	possibly damaging	0.77
R5201:Pcdh1	UTSW	18	38,198,918 (GRCm38)	missense	probably damaging	0.98
R5266:Pcdh1	UTSW	18	38,192,199 (GRCm38)	missense	probably damaging	1.00
R5267:Pcdh1	UTSW	18	38,192,199 (GRCm38)	missense	probably damaging	1.00
R5351:Pcdh1	UTSW	18	38,197,766 (GRCm38)	missense	probably damaging	1.00
R5568:Pcdh1	UTSW	18	38,197,367 (GRCm38)	missense	probably damaging	1.00
R5729:Pcdh1	UTSW	18	38,202,946 (GRCm38)	missense	probably damaging	1.00
R5731:Pcdh1	UTSW	18	38,198,598 (GRCm38)	missense	probably damaging	1.00
R6043:Pcdh1	UTSW	18	38,203,274 (GRCm38)	missense	probably damaging	0.97
R6278:Pcdh1	UTSW	18	38,199,210 (GRCm38)	missense	probably benign	0.29
R6333:Pcdh1	UTSW	18	38,198,807 (GRCm38)	missense	probably benign	0.25
R6498:Pcdh1	UTSW	18	38,197,437 (GRCm38)	missense	probably benign	0.18
R6937:Pcdh1	UTSW	18	38,203,475 (GRCm38)	missense	possibly damaging	0.86
R6994:Pcdh1	UTSW	18	38,198,500 (GRCm38)	missense	probably damaging	1.00
R7242:Pcdh1	UTSW	18	38,203,217 (GRCm38)	missense	probably benign	0.06
R7289:Pcdh1	UTSW	18	38,189,913 (GRCm38)	missense	probably damaging	0.99
R7391:Pcdh1	UTSW	18	38,202,785 (GRCm38)	missense	possibly damaging	0.95
R7702:Pcdh1	UTSW	18	38,203,516 (GRCm38)	missense	unknown
R7738:Pcdh1	UTSW	18	38,197,476 (GRCm38)	missense	probably benign	0.02
R7849:Pcdh1	UTSW	18	38,189,609 (GRCm38)	missense	probably benign	0.01
R7941:Pcdh1	UTSW	18	38,199,080 (GRCm38)	missense	probably damaging	1.00
R8109:Pcdh1	UTSW	18	38,198,996 (GRCm38)	missense	probably damaging	1.00
R8675:Pcdh1	UTSW	18	38,199,176 (GRCm38)	missense	probably damaging	1.00
R8851:Pcdh1	UTSW	18	38,192,102 (GRCm38)	missense	probably damaging	1.00
R8947:Pcdh1	UTSW	18	38,199,020 (GRCm38)	missense	possibly damaging	0.89
R9443:Pcdh1	UTSW	18	38,197,580 (GRCm38)	missense	probably damaging	1.00
R9448:Pcdh1	UTSW	18	38,197,439 (GRCm38)	missense	probably damaging	1.00
R9608:Pcdh1	UTSW	18	38,197,851 (GRCm38)	missense	possibly damaging	0.91
X0027:Pcdh1	UTSW	18	38,189,788 (GRCm38)	nonsense	probably null
Z1088:Pcdh1	UTSW	18	38,198,067 (GRCm38)	missense	probably damaging	1.00
Z1176:Pcdh1	UTSW	18	38,198,688 (GRCm38)	missense	possibly damaging	0.79

Predicted Primers

PCR Primer
(F):5'- AGTCACAACTACCTGGGCAC -3'
(R):5'- GGGCTCTTAGGAAAATAGGTTAGC -3'

Sequencing Primer
(F):5'- TGGGCACGGGCACTCTTG -3'
(R):5'- TCTACTGTAGTGCCAGGCCTAG -3'

Posted On

2014-06-23