Mutagenetix > Incidental Mutation

Incidental Mutation 'R1843:Pcdh1'

207491

Institutional Source

Beutler Lab

Gene Symbol

Pcdh1

Ensembl Gene

ENSMUSG00000051375

Gene Name

protocadherin 1

Synonyms

2010005A06Rik

MMRRC Submission

039868-MU

Accession Numbers

Essential gene?

Possibly non essential (E-score: 0.330) question?

Stock #

R1843 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

38185914-38212053 bp(-) (GRCm38)

Type of Mutation

splice site (4469 bp from exon)

DNA Base Change (assembly)

T to A at 38192225 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Ref Sequence

ENSEMBL: ENSMUSP00000125309 (fasta)

Gene Model

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

AlphaFold

Q8CFX3

Predicted Effect

probably null
Transcript: ENSMUST00000057185

SMART Domains

Protein: ENSMUSP00000055199
Gene: ENSMUSG00000051375

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 null
Transcript: ENSMUST00000159405

SMART Domains

Protein: ENSMUSP00000125309
Gene: ENSMUSG00000051375

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
AA Change: E295V

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)

SMART Domains

Protein: ENSMUSP00000124732
Gene: ENSMUSG00000051375
AA Change: E295V

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: E888V

PolyPhen 2 Score 0.662 (Sensitivity: 0.86; Specificity: 0.91)

SMART Domains

Protein: ENSMUSP00000125576
Gene: ENSMUSG00000051375
AA Change: E888V

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: 97.5%
3x: 96.9%
10x: 95.3%
20x: 92.4%

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: 102 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4933405L10Rik	C	T	8: 105,708,974 (GRCm38)	T88M	probably damaging	Het
9430038I01Rik	A	G	7: 137,377,066 (GRCm38)		probably benign	Het
Adgra3	A	C	5: 49,961,492 (GRCm38)	S905A	probably damaging	Het
Adgrv1	A	G	13: 81,544,533 (GRCm38)	Y1618H	probably damaging	Het
Anapc15-ps	T	C	10: 95,673,314 (GRCm38)	T26A	probably benign	Het
Ankrd13d	T	C	19: 4,271,595 (GRCm38)	K360E	probably damaging	Het
Anks1b	T	A	10: 90,512,889 (GRCm38)		probably null	Het
Apob	T	C	12: 8,007,602 (GRCm38)	F2028S	possibly damaging	Het
Arap3	G	A	18: 37,975,583 (GRCm38)	R1265W	probably damaging	Het
Arhgef37	A	G	18: 61,518,050 (GRCm38)	Y135H	probably damaging	Het
Armh3	A	C	19: 45,975,252 (GRCm38)	S42R	probably benign	Het
Atp1a1	T	C	3: 101,582,017 (GRCm38)	T760A	probably benign	Het
Cdc42bpb	T	A	12: 111,322,821 (GRCm38)	M497L	probably benign	Het
Ces5a	C	T	8: 93,514,231 (GRCm38)	V413M	probably damaging	Het
Chd5	A	T	4: 152,385,806 (GRCm38)	Y1903F	probably damaging	Het
Chd9	T	A	8: 91,010,794 (GRCm38)	N1500K	probably benign	Het
Chmp7	G	T	14: 69,719,799 (GRCm38)	D303E	probably benign	Het
Chrnb4	A	T	9: 55,034,818 (GRCm38)	Y391N	possibly damaging	Het
Crtc1	T	C	8: 70,388,152 (GRCm38)	T475A	probably benign	Het
Cyp2c69	A	G	19: 39,877,528 (GRCm38)	I207T	probably benign	Het
Dcp1a	A	G	14: 30,518,983 (GRCm38)	E250G	probably damaging	Het
Ddx20	T	C	3: 105,679,082 (GRCm38)	Q649R	probably benign	Het
Defb12	T	A	8: 19,112,738 (GRCm38)	K59N	probably damaging	Het
Dpy19l3	A	T	7: 35,729,760 (GRCm38)	I85N	probably damaging	Het
Duox2	C	T	2: 122,292,258 (GRCm38)		probably null	Het
Ebi3	T	A	17: 55,956,679 (GRCm38)	Y197N	probably damaging	Het
Emc1	G	A	4: 139,375,512 (GRCm38)	R994Q	probably benign	Het
Ercc6	G	T	14: 32,546,820 (GRCm38)	M530I	probably damaging	Het
Evl	T	A	12: 108,652,996 (GRCm38)	D70E	probably damaging	Het
Fbln2	A	G	6: 91,265,775 (GRCm38)	N819S	probably damaging	Het
Foxk2	A	G	11: 121,285,537 (GRCm38)	I170V	probably benign	Het
Gfm1	T	C	3: 67,435,610 (GRCm38)	V159A	probably damaging	Het
Gm10837	A	G	14: 122,490,765 (GRCm38)	T18A	unknown	Het
Gm12887	A	T	4: 121,622,030 (GRCm38)	V25E	probably damaging	Het
Hectd4	A	G	5: 121,297,180 (GRCm38)	H985R	possibly damaging	Het
Hsfy2	A	G	1: 56,636,632 (GRCm38)	Y249H	possibly damaging	Het
Hspg2	T	C	4: 137,545,567 (GRCm38)	V2639A	probably damaging	Het
Igf2r	A	G	17: 12,704,270 (GRCm38)		probably null	Het
Invs	T	A	4: 48,422,035 (GRCm38)	I889N	probably damaging	Het
Kcnq1	A	T	7: 143,183,120 (GRCm38)	M209L	probably benign	Het
Klra7	A	G	6: 130,229,994 (GRCm38)	I48T	possibly damaging	Het
Krt26	CTAGTA	CTA	11: 99,333,526 (GRCm38)		probably benign	Het
Lrif1	T	A	3: 106,732,811 (GRCm38)	V404D	probably damaging	Het
Lrriq1	T	A	10: 103,227,173 (GRCm38)		probably null	Het
Lypd6	T	A	2: 50,188,762 (GRCm38)	I90N	possibly damaging	Het
Mbp	A	G	18: 82,584,122 (GRCm38)	D174G	probably damaging	Het
Megf9	G	T	4: 70,534,785 (GRCm38)	P13Q	probably damaging	Het
Myo15b	A	T	11: 115,869,586 (GRCm38)	T1155S	probably benign	Het
Nherf2	C	T	17: 24,641,719 (GRCm38)	S150N	possibly damaging	Het
Nlrp6	T	A	7: 140,923,093 (GRCm38)	C371S	probably damaging	Het
Nosip	T	A	7: 45,077,309 (GRCm38)		probably null	Het
Nox3	G	T	17: 3,669,878 (GRCm38)	P344H	probably damaging	Het
Nup210l	T	C	3: 90,172,086 (GRCm38)	V959A	probably damaging	Het
Olfr175-ps1	T	A	16: 58,824,077 (GRCm38)	I211F	probably damaging	Het
Or10d1	A	G	9: 39,572,735 (GRCm38)	Y175H	possibly damaging	Het
Or2b2b	C	A	13: 21,674,672 (GRCm38)	V91L	probably benign	Het
Or2k2	T	C	4: 58,785,384 (GRCm38)	I113V	probably benign	Het
Or5b119	A	G	19: 13,479,931 (GRCm38)	I89T	probably benign	Het
Osbpl3	A	C	6: 50,370,143 (GRCm38)	S25A	probably damaging	Het
Otog	G	A	7: 46,246,283 (GRCm38)	C107Y	probably damaging	Het
Pax7	G	A	4: 139,784,491 (GRCm38)	R260C	probably damaging	Het
Pbrm1	A	T	14: 31,038,957 (GRCm38)	I224F	probably damaging	Het
Pcnx1	T	C	12: 81,980,935 (GRCm38)	L1585P	probably damaging	Het
Pde4c	C	T	8: 70,747,950 (GRCm38)	H362Y	probably damaging	Het
Pdlim2	C	T	14: 70,164,779 (GRCm38)	R296H	probably damaging	Het
Pgm2	A	T	4: 99,961,478 (GRCm38)	Q90L	probably damaging	Het
Phlpp1	A	G	1: 106,343,505 (GRCm38)	H814R	probably benign	Het
Pknox2	A	T	9: 36,954,831 (GRCm38)	M5K	possibly damaging	Het
Pole	G	A	5: 110,330,835 (GRCm38)		probably null	Het
Polr1b	A	G	2: 129,102,966 (GRCm38)	I61V	probably benign	Het
Prelp	T	C	1: 133,914,757 (GRCm38)	K217E	probably damaging	Het
Prkce	C	T	17: 86,475,546 (GRCm38)	Q202*	probably null	Het
Psmd2	T	G	16: 20,656,582 (GRCm38)	M370R	probably benign	Het
Rimklb	A	T	6: 122,464,009 (GRCm38)	H68Q	probably damaging	Het
Rnasel	A	G	1: 153,754,674 (GRCm38)	D312G	possibly damaging	Het
Rxrg	A	T	1: 167,598,752 (GRCm38)	M1L	probably benign	Het
Scrn1	A	G	6: 54,522,841 (GRCm38)	F220L	possibly damaging	Het
Scyl3	A	G	1: 163,950,675 (GRCm38)	S461G	probably benign	Het
Serpina1c	T	A	12: 103,895,023 (GRCm38)	T411S	probably benign	Het
Serpinb6d	C	T	13: 33,671,381 (GRCm38)	P346L	probably benign	Het
Shld2	A	G	14: 34,267,803 (GRCm38)	I382T	probably benign	Het
Spg21	G	T	9: 65,465,336 (GRCm38)	V17F	probably damaging	Het
Spink5	A	T	18: 43,999,891 (GRCm38)	M525L	probably benign	Het
Sun2	T	C	15: 79,737,563 (GRCm38)	T155A	probably benign	Het
Tchh	T	A	3: 93,446,780 (GRCm38)	F1176I	unknown	Het
Tex15	T	A	8: 33,576,654 (GRCm38)	D2037E	probably benign	Het
Tfdp2	T	C	9: 96,317,804 (GRCm38)	C392R	possibly damaging	Het
Tmem30c	T	C	16: 57,276,780 (GRCm38)	N139S	probably benign	Het
Tns2	C	T	15: 102,113,133 (GRCm38)		probably null	Het
Trim66	T	C	7: 109,475,839 (GRCm38)	E405G	probably damaging	Het
Trpc4	T	A	3: 54,279,994 (GRCm38)	F456I	probably benign	Het
Tspo2	T	C	17: 48,448,790 (GRCm38)	D108G	possibly damaging	Het
Tyk2	A	T	9: 21,121,554 (GRCm38)	C304*	probably null	Het
Vgll4	A	T	6: 114,862,795 (GRCm38)	S185T	probably benign	Het
Vmn2r94	A	C	17: 18,244,470 (GRCm38)	S519R	probably benign	Het
Vmn2r96	T	G	17: 18,597,921 (GRCm38)	S587A	probably benign	Het
Vps4b	C	A	1: 106,778,982 (GRCm38)	A287S	possibly damaging	Het
Yeats2	C	T	16: 20,229,564 (GRCm38)	P1332S	probably benign	Het
Zfp462	T	G	4: 55,010,010 (GRCm38)	S659A	possibly damaging	Het
Zfp507	C	T	7: 35,793,725 (GRCm38)	R631Q	probably damaging	Het
Zfp764l1	A	C	7: 127,391,488 (GRCm38)	D442E	probably benign	Het
Zswim5	G	T	4: 116,877,699 (GRCm38)	E80D	unknown	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
R1839:Pcdh1	UTSW	18	38,199,485 (GRCm38)	missense	possibly damaging	0.82
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'- AAGCTCCTCACCATTCTCGG -3'
(R):5'- ATCTCTGCTAGAGGTTGTGC -3'

Sequencing Primer
(F):5'- ACCATTCTCGGGGTGCTC -3'
(R):5'- CCTATGCTGTACTAAGGGGC -3'

Posted On

2014-06-23