Mutagenetix > Incidental Mutation

Incidental Mutation 'R8947:Pcdh1'

681425

Institutional Source

Beutler Lab

Gene Symbol

Pcdh1

Ensembl Gene

ENSMUSG00000051375

Gene Name

protocadherin 1

Synonyms

2010005A06Rik

MMRRC Submission

068785-MU

Accession Numbers

Essential gene?

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

Stock #

R8947 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

38318967-38345023 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 38332073 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Aspartic acid to Glycine at position 310 (D310G)

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: D449G

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

SMART Domains

Protein: ENSMUSP00000055199
Gene: ENSMUSG00000051375
AA Change: D449G

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: D449G

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

SMART Domains

Protein: ENSMUSP00000125309
Gene: ENSMUSG00000051375
AA Change: D449G

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: D310G

PolyPhen 2 Score 0.895 (Sensitivity: 0.82; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000125576
Gene: ENSMUSG00000051375
AA Change: D310G

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: 100.0%
3x: 99.9%
10x: 99.6%
20x: 98.8%

Validation Efficiency

99% (93/94)

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: 97 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4930562C15Rik	T	A	16: 4,665,292 (GRCm39)	F141L	unknown	Het
A2ml1	G	T	6: 128,529,219 (GRCm39)	N974K	probably damaging	Het
Abcg8	T	C	17: 84,999,246 (GRCm39)	L114P	probably damaging	Het
Akt3	A	T	1: 176,958,645 (GRCm39)	W22R	probably damaging	Het
Ank2	C	T	3: 126,736,396 (GRCm39)		probably benign	Het
Ap1g1	C	T	8: 110,589,964 (GRCm39)		probably benign	Het
Arhgef19	T	A	4: 140,973,618 (GRCm39)	V35E	possibly damaging	Het
Baz2b	T	C	2: 59,778,583 (GRCm39)	D759G	probably benign	Het
BC051665	C	A	13: 60,930,004 (GRCm39)	G320W	probably damaging	Het
Bche	T	A	3: 73,608,761 (GRCm39)	T222S	probably damaging	Het
C8a	T	C	4: 104,679,326 (GRCm39)	D444G	probably damaging	Het
Cacna1e	A	T	1: 154,277,896 (GRCm39)	S2019T	probably benign	Het
Carm1	T	C	9: 21,497,749 (GRCm39)	I373T	probably damaging	Het
Ccdc39	T	C	3: 33,869,609 (GRCm39)		probably benign	Het
Clic5	A	T	17: 44,553,148 (GRCm39)		probably benign	Het
Cntn3	A	G	6: 102,414,864 (GRCm39)	F28L	probably damaging	Het
Col6a5	C	T	9: 105,822,833 (GRCm39)	E175K	unknown	Het
Cpb2	T	C	14: 75,515,627 (GRCm39)	Y352H	probably damaging	Het
Cpeb3	A	T	19: 37,152,366 (GRCm39)	D3E	probably damaging	Het
Ctsl	T	C	13: 64,514,840 (GRCm39)	T155A	probably damaging	Het
Cygb	C	T	11: 116,540,645 (GRCm39)	A114T	probably damaging	Het
Cyp11a1	T	C	9: 57,924,738 (GRCm39)	V17A	probably benign	Het
Dhcr7	T	G	7: 143,400,959 (GRCm39)	I374S	probably damaging	Het
Dhx36	T	C	3: 62,380,387 (GRCm39)	R807G	probably benign	Het
Diaph1	A	T	18: 37,986,754 (GRCm39)	V1077E	probably damaging	Het
Ehmt2	A	G	17: 35,127,280 (GRCm39)	E131G	possibly damaging	Het
Evpl	A	G	11: 116,112,164 (GRCm39)	I1842T	probably damaging	Het
Fastk	C	A	5: 24,646,649 (GRCm39)	C294F	probably damaging	Het
Fndc5	T	C	4: 129,030,929 (GRCm39)	C20R	probably benign	Het
Gm7298	C	A	6: 121,757,553 (GRCm39)	Q1053K	possibly damaging	Het
Gm8362	A	G	14: 18,151,405 (GRCm39)		probably null	Het
Gmps	T	A	3: 63,906,098 (GRCm39)	I465N	probably damaging	Het
Heatr4	T	G	12: 84,001,431 (GRCm39)	M904L	probably benign	Het
Hhip	T	A	8: 80,771,785 (GRCm39)	D175V	probably damaging	Het
Hmcn2	G	A	2: 31,278,220 (GRCm39)	V1641M	probably damaging	Het
Hoxa5	T	G	6: 52,179,776 (GRCm39)	T200P	probably damaging	Het
Ift122	C	A	6: 115,901,368 (GRCm39)	A1050D	probably benign	Het
Igf2bp2	C	A	16: 21,897,473 (GRCm39)	E247*	probably null	Het
Irak1bp1	T	A	9: 82,728,846 (GRCm39)	L259H	probably damaging	Het
Irgm1	G	A	11: 48,759,575 (GRCm39)		probably benign	Het
Itih1	A	T	14: 30,657,866 (GRCm39)		probably benign	Het
Itpk1	A	T	12: 102,536,582 (GRCm39)	C355S	probably benign	Het
Kcng4	T	C	8: 120,352,452 (GRCm39)	E486G	possibly damaging	Het
Kif20b	T	C	19: 34,918,629 (GRCm39)	V671A	possibly damaging	Het
Kif28	T	G	1: 179,544,320 (GRCm39)	I345L	possibly damaging	Het
Klri2	C	G	6: 129,710,742 (GRCm39)		probably null	Het
Kntc1	T	C	5: 123,925,041 (GRCm39)	V1118A	probably benign	Het
Lpin2	T	A	17: 71,511,871 (GRCm39)	I34N	probably benign	Het
Lrch3	T	A	16: 32,802,199 (GRCm39)	V264D	possibly damaging	Het
Lrrk2	C	T	15: 91,586,473 (GRCm39)	Q430*	probably null	Het
Map10	T	G	8: 126,397,839 (GRCm39)	S411A	probably benign	Het
Map1a	A	T	2: 121,135,450 (GRCm39)	I2089F	probably benign	Het
Med12l	T	A	3: 58,984,443 (GRCm39)		probably benign	Het
Mypn	T	A	10: 63,005,156 (GRCm39)	Q317L	probably damaging	Het
Ncan	T	A	8: 70,555,171 (GRCm39)	I999F	probably damaging	Het
Nmrk2	C	A	10: 81,035,539 (GRCm39)	R134L	probably damaging	Het
Or4k42	C	T	2: 111,320,042 (GRCm39)	V154I	probably benign	Het
Or51f1d	T	A	7: 102,701,315 (GRCm39)	V270E	probably damaging	Het
Or5k17	T	C	16: 58,746,433 (GRCm39)	N167S	probably benign	Het
Or6z7	A	G	7: 6,483,246 (GRCm39)	V303A	probably benign	Het
Or8b1c	T	A	9: 38,384,685 (GRCm39)	I214N	probably damaging	Het
Osbpl1a	A	G	18: 12,899,858 (GRCm39)		probably null	Het
Pkn2	C	T	3: 142,517,674 (GRCm39)		probably null	Het
Plch1	T	A	3: 63,691,547 (GRCm39)	M31L	probably damaging	Het
Polg2	A	G	11: 106,659,170 (GRCm39)	F448L	probably damaging	Het
Ppp4r3b	A	G	11: 29,150,758 (GRCm39)	T475A	possibly damaging	Het
Prdm13	C	T	4: 21,678,817 (GRCm39)	E558K	probably damaging	Het
Prdm9	T	A	17: 15,764,270 (GRCm39)	I837F	possibly damaging	Het
R3hdm1	T	A	1: 128,102,694 (GRCm39)	M125K	possibly damaging	Het
Rbm39	A	T	2: 155,990,276 (GRCm39)	V468E	probably damaging	Het
Rnasel	T	A	1: 153,630,777 (GRCm39)	V431E	probably damaging	Het
Rps2	T	A	17: 24,940,227 (GRCm39)	D220E	probably benign	Het
Rsf1	T	C	7: 97,331,059 (GRCm39)		probably benign	Het
Rsph10b	G	T	5: 143,913,952 (GRCm39)	A710S	probably benign	Het
Sez6	A	T	11: 77,844,353 (GRCm39)	T59S	probably damaging	Het
Sf3b1	A	T	1: 55,039,444 (GRCm39)	V727E	probably damaging	Het
Slit2	T	G	5: 48,407,140 (GRCm39)	L857R	probably damaging	Het
Spata31g1	T	A	4: 42,972,097 (GRCm39)	S477T	probably benign	Het
Sspo	T	G	6: 48,425,504 (GRCm39)	C42G	probably damaging	Het
Strc	C	T	2: 121,201,470 (GRCm39)	D1245N	probably benign	Het
Supv3l1	T	A	10: 62,268,118 (GRCm39)	T576S	probably benign	Het
Tecrl	C	T	5: 83,461,154 (GRCm39)	R101Q	probably benign	Het
Tmeff2	A	G	1: 51,220,952 (GRCm39)	Y309C	probably damaging	Het
Tmem43	T	A	6: 91,462,362 (GRCm39)	W316R	probably damaging	Het
Tmigd3	T	C	3: 105,821,554 (GRCm39)	V141A	probably benign	Het
Trav9-1	T	C	14: 53,725,584 (GRCm39)	F8L	probably benign	Het
Trbv5	T	G	6: 41,039,641 (GRCm39)	F82C	probably damaging	Het
Ubtf	T	C	11: 102,205,802 (GRCm39)	N41S	possibly damaging	Het
Uggt1	T	C	1: 36,197,229 (GRCm39)	T1225A	probably benign	Het
Vmn1r72	T	C	7: 11,403,807 (GRCm39)	R214G	possibly damaging	Het
Vmn2r12	T	G	5: 109,234,522 (GRCm39)	K563N	possibly damaging	Het
Vmn2r83	T	C	10: 79,304,873 (GRCm39)	S28P	probably benign	Het
Vwa8	T	G	14: 79,438,552 (GRCm39)	L1875R	probably damaging	Het
Xrcc6	T	A	15: 81,913,866 (GRCm39)	V64E	probably damaging	Het
Zfp292	T	C	4: 34,811,835 (GRCm39)	Y403C	probably damaging	Het
Zfp955a	A	T	17: 33,460,955 (GRCm39)	H392Q	probably damaging	Het
Zfyve19	T	C	2: 119,041,290 (GRCm39)	S69P	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
R2511:Pcdh1	UTSW	18	38,332,532 (GRCm39)	missense	possibly damaging	0.95
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
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'- CGTTAGAGCCAGAGTCAGCATC -3'
(R):5'- TATCAGAGGACGTGGCTGAG -3'

Sequencing Primer
(F):5'- GTCAGCATCACTGGCCGTG -3'
(R):5'- ACGTGGCTGAGGAGACC -3'

Posted On

2021-08-31