Mutagenetix > Incidental Mutation

Incidental Mutation 'R2511:Pcdh1'

253048

Institutional Source

Beutler Lab

Gene Symbol

Pcdh1

Ensembl Gene

ENSMUSG00000051375

Gene Name

protocadherin 1

Synonyms

2010005A06Rik

MMRRC Submission

040417-MU

Accession Numbers

Essential gene?

Possibly non essential (E-score: 0.365) question?

Stock #

R2511 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

38318967-38345023 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

G to A at 38332532 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Threonine to Methionine at position 296 (T296M)

Ref Sequence

ENSEMBL: ENSMUSP00000125309 (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: T296M

PolyPhen 2 Score 0.946 (Sensitivity: 0.80; Specificity: 0.95)

SMART Domains

Protein: ENSMUSP00000055199
Gene: ENSMUSG00000051375
AA Change: T296M

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: T296M

PolyPhen 2 Score 0.946 (Sensitivity: 0.80; Specificity: 0.95)

SMART Domains

Protein: ENSMUSP00000125309
Gene: ENSMUSG00000051375
AA Change: T296M

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

probably benign
Transcript: ENSMUST00000161701
AA Change: T157M

PolyPhen 2 Score 0.255 (Sensitivity: 0.91; Specificity: 0.88)

SMART Domains

Protein: ENSMUSP00000125576
Gene: ENSMUSG00000051375
AA Change: T157M

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

Coding Region Coverage

1x: 99.2%
3x: 98.6%
10x: 97.2%
20x: 94.7%

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: 103 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
9330159F19Rik	T	A	10: 29,097,902 (GRCm39)	C100S	probably damaging	Het
Abcc8	C	T	7: 45,800,204 (GRCm39)	R526H	probably damaging	Het
Acad10	G	A	5: 121,769,630 (GRCm39)	P609S	probably benign	Het
Acod1	A	T	14: 103,288,775 (GRCm39)	D95V	probably damaging	Het
Acsm5	A	T	7: 119,129,677 (GRCm39)	I130F	possibly damaging	Het
Ago4	A	T	4: 126,410,864 (GRCm39)	D208E	probably damaging	Het
Agrn	A	T	4: 156,250,881 (GRCm39)		probably null	Het
Ankar	A	T	1: 72,697,853 (GRCm39)	I791K	probably damaging	Het
Ano10	A	G	9: 122,088,011 (GRCm39)	V364A	probably damaging	Het
Arhgap9	T	C	10: 127,164,854 (GRCm39)		probably null	Het
Arsi	G	A	18: 61,049,666 (GRCm39)	C183Y	probably damaging	Het
Ascl2	T	G	7: 142,521,953 (GRCm39)	E97A	probably damaging	Het
Bcl2a1a	C	T	9: 88,839,506 (GRCm39)	R135W	probably damaging	Het
Bms1	C	T	6: 118,368,114 (GRCm39)		probably null	Het
Bysl	T	A	17: 47,915,260 (GRCm39)	T163S	probably benign	Het
Card10	A	G	15: 78,664,473 (GRCm39)	I821T	probably benign	Het
Cc2d2a	A	T	5: 43,892,737 (GRCm39)	Q1433L	probably damaging	Het
Cchcr1	T	C	17: 35,841,410 (GRCm39)	S809P	probably benign	Het
Ccz1	G	T	5: 143,949,815 (GRCm39)	T70K	probably damaging	Het
Cdc25c	G	C	18: 34,871,292 (GRCm39)	L275V	probably damaging	Het
Cep164	A	T	9: 45,686,547 (GRCm39)	L729Q	probably damaging	Het
Clcn6	A	G	4: 148,101,951 (GRCm39)		probably null	Het
Clcn7	T	A	17: 25,374,420 (GRCm39)	V507E	probably damaging	Het
Cracdl	T	C	1: 37,664,381 (GRCm39)	M506V	probably benign	Het
Ctso	A	C	3: 81,840,041 (GRCm39)	T24P	probably damaging	Het
Dis3l2	A	T	1: 86,917,980 (GRCm39)	N543I	probably benign	Het
Dnah12	A	T	14: 26,491,907 (GRCm39)	Y1114F	possibly damaging	Het
Emx1	A	G	6: 85,181,033 (GRCm39)	D250G	probably benign	Het
Epha4	G	A	1: 77,488,339 (GRCm39)	A47V	possibly damaging	Het
Fam149b	A	C	14: 20,428,524 (GRCm39)	N341T	probably damaging	Het
Fsip2	A	G	2: 82,782,001 (GRCm39)	K62R	probably damaging	Het
Fsip2	T	C	2: 82,816,782 (GRCm39)	S4172P	probably benign	Het
Gbp3	A	G	3: 142,276,343 (GRCm39)	R480G	probably benign	Het
Get3	A	G	8: 85,746,395 (GRCm39)	V151A	possibly damaging	Het
Gja8	T	G	3: 96,827,033 (GRCm39)	T210P	probably damaging	Het
Gm5431	T	A	11: 48,779,536 (GRCm39)	N740I	probably benign	Het
Gm9930	T	C	10: 9,410,446 (GRCm39)		noncoding transcript	Het
Gstt4	C	T	10: 75,650,959 (GRCm39)	C221Y	probably benign	Het
Gzmg	A	T	14: 56,395,832 (GRCm39)	D42E	probably benign	Het
Hoxd12	G	A	2: 74,505,815 (GRCm39)	A129T	possibly damaging	Het
Hs2st1	G	A	3: 144,275,691 (GRCm39)		probably benign	Het
Ifnlr1	G	T	4: 135,432,559 (GRCm39)	D332Y	probably damaging	Het
Igsf10	T	C	3: 59,239,287 (GRCm39)	D298G	probably damaging	Het
Irf1	T	C	11: 53,664,617 (GRCm39)	V108A	probably damaging	Het
Jsrp1	C	G	10: 80,648,140 (GRCm39)	S36T	probably benign	Het
Kcnq5	T	A	1: 21,576,006 (GRCm39)	R233*	probably null	Het
Kif7	T	C	7: 79,352,012 (GRCm39)	K917E	probably damaging	Het
Krt7	A	C	15: 101,310,538 (GRCm39)	I62L	probably benign	Het
Lifr	A	G	15: 7,196,397 (GRCm39)	T194A	probably benign	Het
Ltbp2	T	C	12: 84,851,183 (GRCm39)		probably null	Het
Maco1	A	G	4: 134,531,699 (GRCm39)	S657P	probably damaging	Het
Man2c1	A	G	9: 57,048,672 (GRCm39)		probably null	Het
Met	T	C	6: 17,491,966 (GRCm39)	S243P	probably damaging	Het
Mllt10	C	A	2: 18,069,935 (GRCm39)	D30E	possibly damaging	Het
Mre11a	A	C	9: 14,707,065 (GRCm39)		probably null	Het
Mroh9	A	G	1: 162,866,514 (GRCm39)	S710P	probably benign	Het
Mvk	C	A	5: 114,588,459 (GRCm39)	Y116*	probably null	Het
Myh1	A	G	11: 67,096,423 (GRCm39)	I301V	probably benign	Het
Ncf1	T	C	5: 134,254,552 (GRCm39)	D184G	probably damaging	Het
Nxpe4	T	C	9: 48,304,533 (GRCm39)	F207L	probably damaging	Het
Or2ag18	G	T	7: 106,405,168 (GRCm39)	P167H	probably damaging	Het
Or2y1b	T	G	11: 49,209,048 (GRCm39)	L225R	probably damaging	Het
Or4k51	T	A	2: 111,584,661 (GRCm39)	N22K	probably benign	Het
Or52b1	A	T	7: 104,978,817 (GRCm39)	I194N	probably damaging	Het
Or5b24	T	A	19: 12,912,537 (GRCm39)	M145K	possibly damaging	Het
Or5w14	T	C	2: 87,541,392 (GRCm39)	N286S	probably damaging	Het
Pcdh15	A	G	10: 74,481,828 (GRCm39)	D391G	possibly damaging	Het
Pcdha7	C	A	18: 37,107,786 (GRCm39)	D270E	probably damaging	Het
Pgam1	C	A	19: 41,904,315 (GRCm39)	S137R	probably damaging	Het
Pitpnm2	T	C	5: 124,274,389 (GRCm39)	E240G	probably damaging	Het
Plce1	T	G	19: 38,748,498 (GRCm39)	I1729S	probably damaging	Het
Plppr4	G	T	3: 117,125,355 (GRCm39)	N161K	probably damaging	Het
Pramel27	G	A	4: 143,578,561 (GRCm39)	V274I	probably benign	Het
Prkce	T	A	17: 86,932,754 (GRCm39)	I578N	probably damaging	Het
Prss58	A	C	6: 40,874,734 (GRCm39)	S36A	probably damaging	Het
Ptprm	T	C	17: 67,000,773 (GRCm39)	H1128R	probably damaging	Het
Rgs9	T	C	11: 109,159,798 (GRCm39)	Y178C	probably benign	Het
Rubcn	T	C	16: 32,667,624 (GRCm39)	N179S	probably damaging	Het
Sh3bp1	C	T	15: 78,795,706 (GRCm39)	P612S	probably damaging	Het
Sh3bp5	G	A	14: 31,133,586 (GRCm39)	T82M	probably damaging	Het
Shank2	A	G	7: 143,965,314 (GRCm39)	Y974C	probably damaging	Het
Slc9c1	T	C	16: 45,365,099 (GRCm39)	I144T	possibly damaging	Het
Slf2	T	C	19: 44,930,045 (GRCm39)	I374T	possibly damaging	Het
Snx13	A	G	12: 35,188,080 (GRCm39)	D786G	probably benign	Het
Spcs3	A	G	8: 54,976,389 (GRCm39)	V151A	possibly damaging	Het
Sstr2	A	T	11: 113,515,749 (GRCm39)	I223F	probably damaging	Het
Stac3	T	C	10: 127,339,787 (GRCm39)		probably null	Het
Tas1r2	A	G	4: 139,387,162 (GRCm39)	N207S	probably damaging	Het
Tectb	C	G	19: 55,169,431 (GRCm39)		probably benign	Het
Tgm5	T	C	2: 120,907,429 (GRCm39)	E98G	possibly damaging	Het
Tktl2	A	G	8: 66,965,504 (GRCm39)	E354G	probably benign	Het
Tmem94	G	A	11: 115,682,787 (GRCm39)	R608H	probably damaging	Het
Tnrc6a	G	A	7: 122,770,315 (GRCm39)	V702I	probably damaging	Het
Trappc10	A	G	10: 78,047,357 (GRCm39)	S380P	possibly damaging	Het
Trim24	G	A	6: 37,880,587 (GRCm39)		probably null	Het
Ugt1a2	A	G	1: 88,128,846 (GRCm39)	Y163C	probably damaging	Het
Vmn1r215	A	G	13: 23,260,343 (GRCm39)	I128V	probably benign	Het
Vmn2r50	T	A	7: 9,781,640 (GRCm39)	E368D	possibly damaging	Het
Vmn2r59	T	C	7: 41,693,190 (GRCm39)	N470S	probably damaging	Het
Vps45	T	C	3: 95,948,757 (GRCm39)	T333A	probably benign	Het
Zbtb44	T	A	9: 30,965,539 (GRCm39)	D316E	probably damaging	Het
Zdhhc1	C	T	8: 106,210,190 (GRCm39)	V76M	probably benign	Het
Zfp235	T	C	7: 23,841,549 (GRCm39)	F656S	probably damaging	Het

Other mutations in Pcdh1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00714:Pcdh1	APN	18	38,331,782 (GRCm39)	missense	possibly damaging	0.65
IGL00919:Pcdh1	APN	18	38,335,865 (GRCm39)	nonsense	probably null
IGL01744:Pcdh1	APN	18	38,336,302 (GRCm39)	missense	probably damaging	1.00
PIT4260001:Pcdh1	UTSW	18	38,336,419 (GRCm39)	missense	probably damaging	0.99
R0542:Pcdh1	UTSW	18	38,322,975 (GRCm39)	missense	probably damaging	0.99
R1449:Pcdh1	UTSW	18	38,322,929 (GRCm39)	missense	probably damaging	0.99
R1540:Pcdh1	UTSW	18	38,322,779 (GRCm39)	missense	probably benign	0.01
R1642:Pcdh1	UTSW	18	38,332,283 (GRCm39)	missense	possibly damaging	0.84
R1672:Pcdh1	UTSW	18	38,325,233 (GRCm39)	missense	probably damaging	1.00
R1695:Pcdh1	UTSW	18	38,335,921 (GRCm39)	missense	probably damaging	1.00
R1727:Pcdh1	UTSW	18	38,336,085 (GRCm39)	nonsense	probably null
R1781:Pcdh1	UTSW	18	38,322,977 (GRCm39)	missense	probably damaging	1.00
R1793:Pcdh1	UTSW	18	38,331,938 (GRCm39)	missense	probably damaging	0.99
R1839:Pcdh1	UTSW	18	38,332,538 (GRCm39)	missense	possibly damaging	0.82
R1843:Pcdh1	UTSW	18	38,325,278 (GRCm39)	splice site	probably null
R1882:Pcdh1	UTSW	18	38,335,895 (GRCm39)	missense	possibly damaging	0.49
R2261:Pcdh1	UTSW	18	38,331,710 (GRCm39)	missense	probably benign	0.01
R2262:Pcdh1	UTSW	18	38,331,710 (GRCm39)	missense	probably benign	0.01
R2263:Pcdh1	UTSW	18	38,331,710 (GRCm39)	missense	probably benign	0.01
R2937:Pcdh1	UTSW	18	38,322,815 (GRCm39)	missense	probably benign	0.40
R3941:Pcdh1	UTSW	18	38,332,511 (GRCm39)	missense	probably benign	0.02
R3942:Pcdh1	UTSW	18	38,332,511 (GRCm39)	missense	probably benign	0.02
R4057:Pcdh1	UTSW	18	38,331,950 (GRCm39)	missense	probably damaging	0.98
R4155:Pcdh1	UTSW	18	38,336,159 (GRCm39)	missense	probably damaging	0.99
R4169:Pcdh1	UTSW	18	38,331,358 (GRCm39)	missense	probably damaging	1.00
R4617:Pcdh1	UTSW	18	38,330,913 (GRCm39)	missense	probably benign	0.00
R4690:Pcdh1	UTSW	18	38,336,528 (GRCm39)	missense	probably benign	0.33
R4825:Pcdh1	UTSW	18	38,322,912 (GRCm39)	missense	possibly damaging	0.77
R5201:Pcdh1	UTSW	18	38,331,971 (GRCm39)	missense	probably damaging	0.98
R5266:Pcdh1	UTSW	18	38,325,252 (GRCm39)	missense	probably damaging	1.00
R5267:Pcdh1	UTSW	18	38,325,252 (GRCm39)	missense	probably damaging	1.00
R5351:Pcdh1	UTSW	18	38,330,819 (GRCm39)	missense	probably damaging	1.00
R5568:Pcdh1	UTSW	18	38,330,420 (GRCm39)	missense	probably damaging	1.00
R5729:Pcdh1	UTSW	18	38,335,999 (GRCm39)	missense	probably damaging	1.00
R5731:Pcdh1	UTSW	18	38,331,651 (GRCm39)	missense	probably damaging	1.00
R6043:Pcdh1	UTSW	18	38,336,327 (GRCm39)	missense	probably damaging	0.97
R6278:Pcdh1	UTSW	18	38,332,263 (GRCm39)	missense	probably benign	0.29
R6333:Pcdh1	UTSW	18	38,331,860 (GRCm39)	missense	probably benign	0.25
R6498:Pcdh1	UTSW	18	38,330,490 (GRCm39)	missense	probably benign	0.18
R6937:Pcdh1	UTSW	18	38,336,528 (GRCm39)	missense	possibly damaging	0.86
R6994:Pcdh1	UTSW	18	38,331,553 (GRCm39)	missense	probably damaging	1.00
R7242:Pcdh1	UTSW	18	38,336,270 (GRCm39)	missense	probably benign	0.06
R7289:Pcdh1	UTSW	18	38,322,966 (GRCm39)	missense	probably damaging	0.99
R7391:Pcdh1	UTSW	18	38,335,838 (GRCm39)	missense	possibly damaging	0.95
R7702:Pcdh1	UTSW	18	38,336,569 (GRCm39)	missense	unknown
R7738:Pcdh1	UTSW	18	38,330,529 (GRCm39)	missense	probably benign	0.02
R7849:Pcdh1	UTSW	18	38,322,662 (GRCm39)	missense	probably benign	0.01
R7941:Pcdh1	UTSW	18	38,332,133 (GRCm39)	missense	probably damaging	1.00
R8109:Pcdh1	UTSW	18	38,332,049 (GRCm39)	missense	probably damaging	1.00
R8675:Pcdh1	UTSW	18	38,332,229 (GRCm39)	missense	probably damaging	1.00
R8851:Pcdh1	UTSW	18	38,325,155 (GRCm39)	missense	probably damaging	1.00
R8947:Pcdh1	UTSW	18	38,332,073 (GRCm39)	missense	possibly damaging	0.89
R9443:Pcdh1	UTSW	18	38,330,633 (GRCm39)	missense	probably damaging	1.00
R9448:Pcdh1	UTSW	18	38,330,492 (GRCm39)	missense	probably damaging	1.00
R9608:Pcdh1	UTSW	18	38,330,904 (GRCm39)	missense	possibly damaging	0.91
X0027:Pcdh1	UTSW	18	38,322,841 (GRCm39)	nonsense	probably null
Z1088:Pcdh1	UTSW	18	38,331,120 (GRCm39)	missense	probably damaging	1.00
Z1176:Pcdh1	UTSW	18	38,331,741 (GRCm39)	missense	possibly damaging	0.79

Predicted Primers

PCR Primer
(F):5'- TCTTGATGAGTCACCAGCCC -3'
(R):5'- AAGACTGTACCATGTGCCG -3'

Sequencing Primer
(F):5'- TGATGAGTCACCAGCCCTATGC -3'
(R):5'- TACCATGTGCCGCTTATGGAAAG -3'

Posted On

2014-12-04