Mutagenetix > Incidental Mutation

Incidental Mutation 'R7289:Pcdh1'

566288

Institutional Source

Beutler Lab

Gene Symbol

Pcdh1

Ensembl Gene

ENSMUSG00000051375

Gene Name

protocadherin 1

Synonyms

2010005A06Rik

MMRRC Submission

045396-MU

Accession Numbers

Essential gene?

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

Stock #

R7289 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

38318967-38345023 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 38322966 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Threonine to Alanine at position 956 (T956A)

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

probably damaging
Transcript: ENSMUST00000161701
AA Change: T956A

PolyPhen 2 Score 0.988 (Sensitivity: 0.73; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000125576
Gene: ENSMUSG00000051375
AA Change: T956A

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: 100.0%
3x: 100.0%
10x: 99.7%
20x: 99.0%

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: 93 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Aars2	G	A	17: 45,818,550 (GRCm39)	D112N	probably damaging	Het
Abca7	T	A	10: 79,845,778 (GRCm39)	I1580K	probably damaging	Het
Aebp1	A	G	11: 5,815,059 (GRCm39)	D234G	probably damaging	Het
Agap1	T	A	1: 89,383,153 (GRCm39)	M1K	probably null	Het
Agrn	A	T	4: 156,263,389 (GRCm39)	L345H	probably damaging	Het
Amfr	A	G	8: 94,725,754 (GRCm39)	M209T	possibly damaging	Het
Angel2	G	A	1: 190,673,371 (GRCm39)	R338H	possibly damaging	Het
Ankrd27	C	T	7: 35,330,674 (GRCm39)	A866V	probably damaging	Het
Apc	G	A	18: 34,448,324 (GRCm39)	R1740Q	probably damaging	Het
Arhgap32	A	T	9: 32,168,233 (GRCm39)	S739C	possibly damaging	Het
Arhgap32	G	C	9: 32,168,234 (GRCm39)	S739T	probably benign	Het
Arhgef2	C	T	3: 88,543,192 (GRCm39)	S418L	probably benign	Het
Arhgef25	T	C	10: 127,019,641 (GRCm39)	T472A	possibly damaging	Het
Atrnl1	C	T	19: 57,638,846 (GRCm39)	S328F	probably benign	Het
Bahcc1	C	T	11: 120,171,000 (GRCm39)	A1514V	probably benign	Het
Calcoco2	C	T	11: 95,990,823 (GRCm39)	E305K	unknown	Het
Ccn1	C	T	3: 145,354,428 (GRCm39)	W161*	probably null	Het
Cdc42bpa	A	T	1: 179,889,362 (GRCm39)	K203*	probably null	Het
Cmc1	A	T	9: 117,904,250 (GRCm39)	I47N	possibly damaging	Het
Cntln	A	G	4: 84,964,540 (GRCm39)	E656G	possibly damaging	Het
Dcun1d3	T	C	7: 119,458,864 (GRCm39)	K57R	possibly damaging	Het
Ddx23	T	C	15: 98,546,492 (GRCm39)	E559G	probably damaging	Het
Dennd6a	G	A	14: 26,333,193 (GRCm39)	R367Q	probably damaging	Het
Desi2	A	T	1: 178,083,702 (GRCm39)		probably benign	Het
Dido1	T	C	2: 180,301,424 (GRCm39)	D2160G	unknown	Het
Efcab3	T	C	11: 104,929,184 (GRCm39)	M4838T	probably benign	Het
Epb41	A	G	4: 131,718,520 (GRCm39)		probably null	Het
Esrrb	T	A	12: 86,517,331 (GRCm39)		probably null	Het
Fabp1	C	A	6: 71,180,111 (GRCm39)	T94N	probably benign	Het
Fam120a	A	T	13: 49,045,482 (GRCm39)	C785S	probably damaging	Het
Fam243	T	C	16: 92,117,710 (GRCm39)	I193V	probably damaging	Het
Foxc1	A	G	13: 31,991,243 (GRCm39)	Y18C	probably damaging	Het
Fshr	T	C	17: 89,293,272 (GRCm39)	T469A	probably benign	Het
Gm14399	T	A	2: 174,972,204 (GRCm39)	H517L	unknown	Het
Gm39115	G	T	7: 141,689,297 (GRCm39)	Q159K	unknown	Het
Gm7347	T	A	5: 26,262,306 (GRCm39)	I72F	possibly damaging	Het
Hmcn1	A	G	1: 150,559,466 (GRCm39)	V2395A	possibly damaging	Het
Ighv5-17	T	G	12: 113,822,858 (GRCm39)	T88P	probably damaging	Het
Insm2	T	A	12: 55,647,329 (GRCm39)	Y358N	probably damaging	Het
Kazn	A	T	4: 141,844,486 (GRCm39)	L409Q		Het
Kcnj5	A	C	9: 32,234,045 (GRCm39)	L90R	probably damaging	Het
Kcnv2	A	T	19: 27,311,084 (GRCm39)	T484S	probably damaging	Het
Kdm3b	T	C	18: 34,927,557 (GRCm39)	Y140H	probably benign	Het
Kifbp	A	C	10: 62,401,895 (GRCm39)	C261W	probably damaging	Het
Krt25	C	T	11: 99,212,098 (GRCm39)	A180T	probably benign	Het
Mmp1a	A	G	9: 7,467,294 (GRCm39)	E290G	probably damaging	Het
Muc21	G	A	17: 35,929,761 (GRCm39)	A1475V	unknown	Het
Nr3c1	T	C	18: 39,547,654 (GRCm39)	T755A	probably benign	Het
Nr3c1	A	T	18: 39,555,786 (GRCm39)	I517N	probably benign	Het
Nxpe2	A	G	9: 48,234,339 (GRCm39)		probably null	Het
Oaz1	C	A	10: 80,662,673 (GRCm39)	T27K	possibly damaging	Het
Or4p7	A	T	2: 88,222,050 (GRCm39)	H153L	probably damaging	Het
Or51f5	T	C	7: 102,424,634 (GRCm39)	I301T	probably damaging	Het
Or5t5	G	T	2: 86,617,034 (GRCm39)	C320F	probably benign	Het
Or6z3	T	A	7: 6,463,777 (GRCm39)	W90R	probably benign	Het
Or8k21	A	G	2: 86,145,369 (GRCm39)	M87T	probably benign	Het
Or8s5	A	G	15: 98,237,943 (GRCm39)	V309A	probably damaging	Het
Pafah2	A	T	4: 134,147,308 (GRCm39)	K319M	probably damaging	Het
Pask	A	T	1: 93,259,309 (GRCm39)	V236E	probably damaging	Het
Pcdhb18	C	A	18: 37,623,700 (GRCm39)	N343K	probably damaging	Het
Pcsk2	A	T	2: 143,532,343 (GRCm39)	I164F	probably damaging	Het
Phf1	T	C	17: 27,154,289 (GRCm39)	Y169H	probably damaging	Het
Pkdrej	T	A	15: 85,705,301 (GRCm39)	I212F	probably benign	Het
Pnkp	T	A	7: 44,508,114 (GRCm39)	W146R	probably damaging	Het
Prkcb	A	T	7: 122,143,910 (GRCm39)	I325F	probably benign	Het
Ptpn21	C	T	12: 98,670,450 (GRCm39)	D239N	probably benign	Het
Ptprb	A	G	10: 116,164,070 (GRCm39)	T626A	probably damaging	Het
Pttg1	T	C	11: 43,311,916 (GRCm39)	N180D	probably benign	Het
Raly	G	A	2: 154,703,774 (GRCm39)	R115Q	probably damaging	Het
Rims2	A	T	15: 39,301,114 (GRCm39)	M474L	probably benign	Het
Sash1	A	T	10: 8,605,960 (GRCm39)	I810N	probably damaging	Het
Scnn1g	T	A	7: 121,337,304 (GRCm39)	L55*	probably null	Het
Sema6b	A	T	17: 56,432,573 (GRCm39)	D543E	possibly damaging	Het
Serpina11	C	T	12: 103,952,761 (GRCm39)	G5E	unknown	Het
Sesn3	A	T	9: 14,187,848 (GRCm39)	M1L	probably benign	Het
Sez6	T	A	11: 77,865,149 (GRCm39)	I632N	possibly damaging	Het
Sgo2b	A	T	8: 64,394,192 (GRCm39)	I49N	probably damaging	Het
Slc30a2	A	T	4: 134,071,524 (GRCm39)	I86F	possibly damaging	Het
Slc38a6	T	A	12: 73,333,786 (GRCm39)	W30R	probably benign	Het
Spata31g1	A	T	4: 42,972,379 (GRCm39)	T571S	probably benign	Het
Spata31g1	A	T	4: 42,973,252 (GRCm39)	I862F	possibly damaging	Het
Stk31	T	G	6: 49,415,393 (GRCm39)	V576G	probably benign	Het
Szt2	G	A	4: 118,233,075 (GRCm39)	T2297I	unknown	Het
Tmem208	T	C	8: 106,061,418 (GRCm39)	F148S	possibly damaging	Het
Tprg1l	A	G	4: 154,245,031 (GRCm39)	L19P	possibly damaging	Het
Tubg2	C	A	11: 101,050,897 (GRCm39)	N207K	probably damaging	Het
Ube2n	G	T	10: 95,377,612 (GRCm39)	K130N	probably benign	Het
Usp36	T	C	11: 118,164,355 (GRCm39)	Y384C	probably damaging	Het
Vcan	A	T	13: 89,840,852 (GRCm39)	L1564*	probably null	Het
Xkr6	A	T	14: 64,035,748 (GRCm39)	D283V	unknown	Het
Zfp654	T	C	16: 64,605,523 (GRCm39)	H352R	probably benign	Het
Zfp819	T	A	7: 43,266,506 (GRCm39)	C330S	probably damaging	Het
Zfp970	G	T	2: 177,167,086 (GRCm39)	C220F	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
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'- TCATGGCTACTGTGGGAGAAG -3'
(R):5'- TAAGGAAGGCTGTGCTTGC -3'

Sequencing Primer
(F):5'- CTACTGTGGGAGAAGGCACTG -3'
(R):5'- GGCTGTGCTTGCCTGAG -3'

Posted On

2019-06-26