Mutagenetix > Incidental Mutation

Incidental Mutation 'R7011:Pcdha1'

545053

Institutional Source

Beutler Lab

Gene Symbol

Pcdha1

Ensembl Gene

ENSMUSG00000103442

Gene Name

protocadherin alpha 1

Synonyms

MMRRC Submission

045112-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R7011 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

37063338-37320710 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 37063588 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Isoleucine to Threonine at position 84 (I84T)

Ref Sequence

ENSEMBL: ENSMUSP00000142308 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000070797] [ENSMUST00000193839]

AlphaFold

Q91Y21

Predicted Effect

probably damaging
Transcript: ENSMUST00000070797
AA Change: I84T

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000068828
Gene: ENSMUSG00000103442
AA Change: I84T

Domain	Start	End	E-Value	Type
CA	22	132	3.09e-2	SMART
CA	156	241	6.14e-20	SMART
CA	265	349	3.92e-27	SMART
CA	373	454	4.94e-24	SMART
CA	478	564	1e-24	SMART
CA	592	672	4.55e-14	SMART
transmembrane domain	694	716	N/A	INTRINSIC
Pfam:Cadherin_tail	797	931	5.3e-58	PFAM

Predicted Effect

probably damaging
Transcript: ENSMUST00000193839
AA Change: I84T

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000142308
Gene: ENSMUSG00000103442
AA Change: I84T

Domain	Start	End	E-Value	Type
CA	22	132	3.09e-2	SMART
CA	156	241	6.14e-20	SMART
CA	265	349	3.92e-27	SMART
CA	373	454	4.94e-24	SMART
CA	478	564	1e-24	SMART
CA	592	672	4.55e-14	SMART
transmembrane domain	694	716	N/A	INTRINSIC

Coding Region Coverage

1x: 100.0%
3x: 100.0%
10x: 99.7%
20x: 98.9%

Validation Efficiency

96% (66/69)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene is a member of the protocadherin alpha gene cluster, one of three related gene clusters tandemly linked on chromosome five that demonstrate an unusual genomic organization similar to that of B-cell and T-cell receptor gene clusters. The alpha gene cluster is composed of 15 cadherin superfamily genes related to the mouse CNR genes and consists of 13 highly similar and 2 more distantly related coding sequences. The tandem array of 15 N-terminal exons, or variable exons, are followed by downstream C-terminal exons, or constant exons, which are shared by all genes in the cluster. The large, uninterrupted N-terminal exons each encode six cadherin ectodomains while the C-terminal exons encode the cytoplasmic domain. These neural cadherin-like cell adhesion proteins are integral plasma membrane proteins that most likely play a critical role in the establishment and function of specific cell-cell connections in the brain. Alternative splicing has been observed and additional variants have been suggested but their full-length nature has yet to be determined. [provided by RefSeq, Jul 2008]
PHENOTYPE: Mice homozygous for a null allele are viable and fertile. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 68 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Adam19	C	T	11: 46,033,845 (GRCm39)	P886S	probably benign	Het
Anapc1	C	T	2: 128,490,601 (GRCm39)		probably null	Het
Ankrd34c	C	A	9: 89,611,001 (GRCm39)	G447*	probably null	Het
Apbb1ip	A	T	2: 22,725,943 (GRCm39)	E238D	probably damaging	Het
Arfgap1	T	C	2: 180,613,935 (GRCm39)	L110P	probably damaging	Het
Arhgap21	G	A	2: 20,853,689 (GRCm39)	T1901I	possibly damaging	Het
Brpf1	C	A	6: 113,295,427 (GRCm39)	Q679K	probably benign	Het
Btnl2	A	G	17: 34,582,487 (GRCm39)	E351G	probably damaging	Het
Cd209f	T	A	8: 4,154,859 (GRCm39)	T80S	probably benign	Het
Cdc16	A	G	8: 13,819,451 (GRCm39)	E349G	probably damaging	Het
Cfap53	A	T	18: 74,462,564 (GRCm39)	D436V	probably benign	Het
Crhr2	A	T	6: 55,076,195 (GRCm39)		probably null	Het
Cux1	T	C	5: 136,388,887 (GRCm39)	K226E	probably damaging	Het
Ddr2	A	T	1: 169,809,672 (GRCm39)	D768E	probably damaging	Het
Dhx8	T	C	11: 101,632,346 (GRCm39)	L435P	probably damaging	Het
Dnah11	AGGCC	AGGCCGGCC	12: 117,885,753 (GRCm39)		probably null	Het
Eif4ebp1	G	A	8: 27,763,372 (GRCm39)	R55Q	probably damaging	Het
Fbh1	T	A	2: 11,767,774 (GRCm39)	D358V	probably damaging	Het
Fra10ac1	T	A	19: 38,177,242 (GRCm39)	E304D	probably benign	Het
Gabrb2	T	C	11: 42,517,488 (GRCm39)	S399P	possibly damaging	Het
Gpatch2l	G	A	12: 86,290,958 (GRCm39)	R47H	probably damaging	Het
Gprin2	G	T	14: 33,917,393 (GRCm39)	H126N	probably null	Het
Gucy1a1	A	G	3: 82,016,422 (GRCm39)	S189P	probably damaging	Het
Htr1d	T	C	4: 136,170,317 (GRCm39)	M182T	probably benign	Het
Lipc	A	G	9: 70,726,236 (GRCm39)	F73L	probably benign	Het
Liph	A	G	16: 21,802,847 (GRCm39)	I74T	probably damaging	Het
Lrif1	T	G	3: 106,639,601 (GRCm39)	Y229D	probably damaging	Het
Magel2	C	T	7: 62,028,281 (GRCm39)	T395I	possibly damaging	Het
Magi3	T	C	3: 104,013,070 (GRCm39)	N139S	probably damaging	Het
Man2c1	T	A	9: 57,045,117 (GRCm39)	V336E	probably damaging	Het
Mapk12	A	T	15: 89,019,803 (GRCm39)	Y135N	probably damaging	Het
Mapkapk3	C	T	9: 107,166,595 (GRCm39)		probably benign	Het
Mast1	A	T	8: 85,638,574 (GRCm39)	Y653*	probably null	Het
Muc16	T	A	9: 18,548,839 (GRCm39)	H5818L	probably benign	Het
Muc16	T	A	9: 18,548,747 (GRCm39)	I5849F	probably benign	Het
Ndufa10	A	G	1: 92,398,581 (GRCm39)	S68P	probably damaging	Het
Nedd1	C	A	10: 92,526,635 (GRCm39)	L503F	probably benign	Het
Nr1i3	A	G	1: 171,041,927 (GRCm39)	M4V	probably benign	Het
Or12e9	G	A	2: 87,202,604 (GRCm39)	A243T	possibly damaging	Het
Or2av9	T	A	11: 58,380,970 (GRCm39)	I204F	possibly damaging	Het
Or4f14b	A	T	2: 111,775,031 (GRCm39)	F257I	probably benign	Het
Or9i2	T	C	19: 13,816,403 (GRCm39)	I45V	probably benign	Het
Pcdh18	A	T	3: 49,709,231 (GRCm39)	S695T	probably benign	Het
Plek	T	A	11: 16,944,760 (GRCm39)	D90V	possibly damaging	Het
Ppp6r1	A	G	7: 4,649,825 (GRCm39)	C47R	probably damaging	Het
Psg27	G	C	7: 18,290,798 (GRCm39)	N468K	probably benign	Het
Ptchd4	G	A	17: 42,814,759 (GRCm39)	E887K	probably benign	Het
Rabgap1	C	T	2: 37,430,492 (GRCm39)	L678F	probably damaging	Het
Rmdn3	T	C	2: 118,968,904 (GRCm39)	Y429C	probably damaging	Het
Ros1	A	T	10: 52,056,272 (GRCm39)	C73S	probably damaging	Het
Rtkn2	G	A	10: 67,815,495 (GRCm39)		probably benign	Het
Slc25a42	A	G	8: 70,639,352 (GRCm39)	S242P	probably damaging	Het
Smtnl1	T	A	2: 84,648,753 (GRCm39)	D167V	probably benign	Het
Smurf2	A	G	11: 106,724,610 (GRCm39)	L511P	probably benign	Het
Stbd1	A	T	5: 92,752,977 (GRCm39)	K156*	probably null	Het
Tenm4	G	T	7: 96,545,342 (GRCm39)	G2453*	probably null	Het
Tent4a	C	T	13: 69,648,199 (GRCm39)	G489S	probably damaging	Het
Tpr	A	G	1: 150,309,523 (GRCm39)	K1760E	probably damaging	Het
Triobp	T	A	15: 78,862,923 (GRCm39)	L1427Q	probably damaging	Het
Uaca	A	G	9: 60,777,650 (GRCm39)	E679G	probably damaging	Het
Ucn3	T	G	13: 3,991,421 (GRCm39)	H77P	possibly damaging	Het
Wnk2	T	A	13: 49,224,567 (GRCm39)	D998V	probably damaging	Het
Xrcc3	A	G	12: 111,770,969 (GRCm39)	V320A	probably damaging	Het
Zdbf2	A	G	1: 63,345,925 (GRCm39)	T1435A	possibly damaging	Het
Zfp36l2	G	T	17: 84,493,861 (GRCm39)	H259N	possibly damaging	Het
Zfp619	A	T	7: 39,187,186 (GRCm39)	H1072L	probably damaging	Het
Zfy2	T	A	Y: 2,107,127 (GRCm39)	E502D	possibly damaging	Het
Zfyve16	G	A	13: 92,658,495 (GRCm39)	P472L	probably benign	Het

Other mutations in Pcdha1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00714:Pcdha1	APN	18	37,065,228 (GRCm39)	missense	probably damaging	0.99
R0062:Pcdha1	UTSW	18	37,139,681 (GRCm39)	missense	probably benign	0.08
R0108:Pcdha1	UTSW	18	37,131,809 (GRCm39)	missense	probably benign
R0543:Pcdha1	UTSW	18	37,318,121 (GRCm39)	missense	probably damaging	1.00
R1599:Pcdha1	UTSW	18	37,318,290 (GRCm39)	missense	probably damaging	1.00
R1717:Pcdha1	UTSW	18	37,065,237 (GRCm39)	missense	probably benign	0.01
R2301:Pcdha1	UTSW	18	37,289,236 (GRCm39)	missense	probably damaging	1.00
R3038:Pcdha1	UTSW	18	37,064,064 (GRCm39)	missense	probably damaging	1.00
R3086:Pcdha1	UTSW	18	37,064,001 (GRCm39)	missense	possibly damaging	0.95
R3693:Pcdha1	UTSW	18	37,065,361 (GRCm39)	missense	possibly damaging	0.95
R3783:Pcdha1	UTSW	18	37,063,855 (GRCm39)	missense	probably damaging	1.00
R3881:Pcdha1	UTSW	18	37,064,454 (GRCm39)	missense	possibly damaging	0.91
R4012:Pcdha1	UTSW	18	37,064,189 (GRCm39)	missense	probably benign	0.02
R4540:Pcdha1	UTSW	18	37,064,680 (GRCm39)	missense	probably damaging	1.00
R4597:Pcdha1	UTSW	18	37,064,959 (GRCm39)	missense	possibly damaging	0.64
R4678:Pcdha1	UTSW	18	37,063,965 (GRCm39)	missense	probably benign	0.00
R4998:Pcdha1	UTSW	18	37,065,469 (GRCm39)	missense	probably damaging	1.00
R5466:Pcdha1	UTSW	18	37,065,312 (GRCm39)	missense	possibly damaging	0.73
R5518:Pcdha1	UTSW	18	37,065,415 (GRCm39)	missense	probably benign	0.23
R5673:Pcdha1	UTSW	18	37,063,726 (GRCm39)	missense	probably damaging	1.00
R5925:Pcdha1	UTSW	18	37,063,724 (GRCm39)	missense	probably damaging	1.00
R5942:Pcdha1	UTSW	18	37,063,444 (GRCm39)	missense	probably damaging	1.00
R5963:Pcdha1	UTSW	18	37,064,224 (GRCm39)	missense	probably damaging	0.99
R6034:Pcdha1	UTSW	18	37,063,651 (GRCm39)	missense	probably damaging	1.00
R6034:Pcdha1	UTSW	18	37,063,651 (GRCm39)	missense	probably damaging	1.00
R6107:Pcdha1	UTSW	18	37,065,354 (GRCm39)	missense	probably benign	0.00
R6329:Pcdha1	UTSW	18	37,065,301 (GRCm39)	missense	probably damaging	1.00
R6479:Pcdha1	UTSW	18	37,064,509 (GRCm39)	missense	probably benign	0.28
R6503:Pcdha1	UTSW	18	37,064,724 (GRCm39)	missense	probably damaging	1.00
R6907:Pcdha1	UTSW	18	37,064,124 (GRCm39)	missense	probably benign	0.01
R7030:Pcdha1	UTSW	18	37,292,326 (GRCm39)	missense	probably damaging	0.97
R7314:Pcdha1	UTSW	18	37,064,553 (GRCm39)	missense	probably damaging	0.99
R7343:Pcdha1	UTSW	18	37,063,702 (GRCm39)	missense	probably damaging	1.00
R7699:Pcdha1	UTSW	18	37,064,115 (GRCm39)	missense	probably damaging	0.98
R7700:Pcdha1	UTSW	18	37,064,115 (GRCm39)	missense	probably damaging	0.98
R7768:Pcdha1	UTSW	18	37,065,220 (GRCm39)	missense	probably damaging	1.00
R7780:Pcdha1	UTSW	18	37,065,511 (GRCm39)	missense	probably benign	0.28
R7800:Pcdha1	UTSW	18	37,064,426 (GRCm39)	missense	probably damaging	1.00
R7917:Pcdha1	UTSW	18	37,065,254 (GRCm39)	missense	possibly damaging	0.64
R8325:Pcdha1	UTSW	18	37,063,867 (GRCm39)	missense	possibly damaging	0.47
R8699:Pcdha1	UTSW	18	37,064,076 (GRCm39)	missense	probably benign	0.00
R9400:Pcdha1	UTSW	18	37,064,760 (GRCm39)	missense	probably benign	0.43
R9513:Pcdha1	UTSW	18	37,065,286 (GRCm39)	missense	probably benign	0.26
R9746:Pcdha1	UTSW	18	37,065,713 (GRCm39)	missense	probably benign

Predicted Primers

PCR Primer
(F):5'- AGCGGCCAGATTCATTACTC -3'
(R):5'- ATTGGCACCAATGTCTGCGTC -3'

Sequencing Primer
(F):5'- GGCCAGATTCATTACTCTGTCCCAG -3'
(R):5'- CCTCTAGTGGAAACCGTGAATCTAG -3'

Posted On

2019-05-13