Mutagenetix > Incidental Mutation

Incidental Mutation 'R9781:Pcdha2'

734086

Institutional Source

Beutler Lab

Gene Symbol

Pcdha2

Ensembl Gene

ENSMUSG00000104148

Gene Name

protocadherin alpha 2

Synonyms

MMRRC Submission

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.182) question?

Stock #

R9781 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

37072258-37320710 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 37074102 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Serine to Glycine at position 578 (S578G)

Ref Sequence

ENSEMBL: ENSMUSP00000111326 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000070797] [ENSMUST00000115662] [ENSMUST00000193839] [ENSMUST00000195590]

AlphaFold

Q91Y17

Predicted Effect

probably benign
Transcript: ENSMUST00000070797

SMART Domains

Protein: ENSMUSP00000068828
Gene: ENSMUSG00000103442

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 benign
Transcript: ENSMUST00000115662
AA Change: S578G

PolyPhen 2 Score 0.085 (Sensitivity: 0.93; Specificity: 0.85)

SMART Domains

Protein: ENSMUSP00000111326
Gene: ENSMUSG00000104148
AA Change: S578G

Domain	Start	End	E-Value	Type
CA	45	131	6.34e-2	SMART
CA	155	240	2.98e-18	SMART
CA	264	348	2.17e-29	SMART
CA	372	453	2.84e-24	SMART
CA	477	563	5.02e-25	SMART
CA	594	675	8.16e-16	SMART
transmembrane domain	695	717	N/A	INTRINSIC
low complexity region	916	940	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000193839

SMART Domains

Protein: ENSMUSP00000142308
Gene: ENSMUSG00000103442

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

Predicted Effect

probably benign
Transcript: ENSMUST00000195590
AA Change: S578G

PolyPhen 2 Score 0.279 (Sensitivity: 0.91; Specificity: 0.88)

SMART Domains

Protein: ENSMUSP00000141355
Gene: ENSMUSG00000104148
AA Change: S578G

Domain	Start	End	E-Value	Type
CA	45	131	6.34e-2	SMART
CA	155	240	2.98e-18	SMART
CA	264	348	2.17e-29	SMART
CA	372	453	2.84e-24	SMART
CA	477	563	5.02e-25	SMART
CA	594	675	8.16e-16	SMART
transmembrane domain	695	717	N/A	INTRINSIC

Coding Region Coverage

1x: 99.9%
3x: 99.8%
10x: 99.3%
20x: 98.1%

Validation Efficiency

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]

Allele List at MGI

Other mutations in this stock

Total: 72 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
A2ml1	A	G	6: 128,519,860 (GRCm39)	F1386L	probably benign	Het
Aoc1l2	G	A	6: 48,907,660 (GRCm39)	S220N	possibly damaging	Het
Ap3d1	A	C	10: 80,545,609 (GRCm39)	L1040R	possibly damaging	Het
Bag4	T	A	8: 26,259,564 (GRCm39)	N212Y	probably damaging	Het
Bop1	A	T	15: 76,338,041 (GRCm39)	S610T	probably damaging	Het
Car12	T	G	9: 66,624,844 (GRCm39)	S30A	probably benign	Het
Ccdc14	A	T	16: 34,543,984 (GRCm39)	T829S	possibly damaging	Het
Ccn6	T	A	10: 39,027,167 (GRCm39)	*355L	probably null	Het
Cdc14a	A	T	3: 116,122,274 (GRCm39)	I231N	probably benign	Het
Ceacam14	A	T	7: 17,549,082 (GRCm39)	I158F	possibly damaging	Het
Clca4a	G	T	3: 144,667,713 (GRCm39)	S419R	probably benign	Het
Clec2g	A	G	6: 128,960,012 (GRCm39)	N258D	probably benign	Het
Cntn5	A	C	9: 10,048,686 (GRCm39)		probably null	Het
Col5a3	T	A	9: 20,721,272 (GRCm39)	S72C	unknown	Het
Dmbt1	G	C	7: 130,639,599 (GRCm39)	V46L	probably benign	Het
Dnah7b	A	G	1: 46,376,754 (GRCm39)		probably null	Het
Dnase1	T	C	16: 3,857,054 (GRCm39)	S204P	probably benign	Het
Dnhd1	A	G	7: 105,352,917 (GRCm39)	E2690G	probably benign	Het
Dst	T	C	1: 34,218,075 (GRCm39)	L1505P	probably benign	Het
Dzip1	G	A	14: 119,148,834 (GRCm39)	L282F	probably benign	Het
E330034G19Rik	A	G	14: 24,359,528 (GRCm39)	E313G	unknown	Het
Epc1	A	T	18: 6,455,187 (GRCm39)		probably null	Het
Herc1	T	C	9: 66,280,004 (GRCm39)	M304T	probably benign	Het
Herc2	A	T	7: 55,750,096 (GRCm39)	I594F	possibly damaging	Het
Hivep2	T	A	10: 14,005,828 (GRCm39)	S809T	probably benign	Het
Hnrnph3	A	T	10: 62,853,861 (GRCm39)	M132K	unknown	Het
Hrnr	A	T	3: 93,239,696 (GRCm39)	R3311S	unknown	Het
Jph3	T	C	8: 122,457,380 (GRCm39)	F7L	probably damaging	Het
Med13l	C	T	5: 118,868,032 (GRCm39)	T732M	possibly damaging	Het
Mocos	A	T	18: 24,828,939 (GRCm39)	H748L	probably benign	Het
Mrc1	A	G	2: 14,249,100 (GRCm39)	H212R	probably benign	Het
Mrc1	A	T	2: 14,310,175 (GRCm39)	Y812F	possibly damaging	Het
Mthfr	T	C	4: 148,132,710 (GRCm39)	I296T	probably damaging	Het
Ncdn	G	A	4: 126,642,467 (GRCm39)	R397W	probably damaging	Het
Nefh	G	A	11: 4,895,271 (GRCm39)	T306I	probably damaging	Het
Nme7	C	A	1: 164,155,890 (GRCm39)	A30E	possibly damaging	Het
Or52z15	T	A	7: 103,332,246 (GRCm39)	M97K	probably damaging	Het
Pappa	T	A	4: 65,043,104 (GRCm39)	L109Q	possibly damaging	Het
Pcf11	A	T	7: 92,297,228 (GRCm39)	D1361E	possibly damaging	Het
Pcm1	T	C	8: 41,720,398 (GRCm39)	S320P	probably damaging	Het
Pex19	T	A	1: 171,956,855 (GRCm39)	F105Y	probably damaging	Het
Pgap4	C	T	4: 49,586,890 (GRCm39)	V93I	probably benign	Het
Pggt1b	A	T	18: 46,392,779 (GRCm39)	M124K	probably damaging	Het
Phkg1	T	A	5: 129,895,807 (GRCm39)	H148L	probably damaging	Het
Phlpp2	G	T	8: 110,662,178 (GRCm39)	R855L	possibly damaging	Het
Pkhd1	T	A	1: 20,187,665 (GRCm39)	I3548L	possibly damaging	Het
Plce1	T	G	19: 38,513,654 (GRCm39)	S318A	probably damaging	Het
Plcxd2	A	G	16: 45,830,117 (GRCm39)	W35R	probably benign	Het
Prl2b1	T	A	13: 27,569,129 (GRCm39)	E156D	possibly damaging	Het
Ptpn21	A	G	12: 98,655,170 (GRCm39)	V599A	probably damaging	Het
Raly	T	C	2: 154,699,265 (GRCm39)	V23A	probably damaging	Het
Rapgef3	T	C	15: 97,643,479 (GRCm39)	I911V	probably damaging	Het
Rhbdl1	A	G	17: 26,055,443 (GRCm39)	V48A	probably benign	Het
Rhpn1	C	T	15: 75,582,543 (GRCm39)	Q212*	probably null	Het
Sec24b	G	T	3: 129,789,742 (GRCm39)	P760T	probably damaging	Het
Septin8	C	A	11: 53,422,889 (GRCm39)	Q33K	probably damaging	Het
Serpinb6a	T	C	13: 34,109,346 (GRCm39)	T150A	probably benign	Het
Shmt1	A	T	11: 60,692,329 (GRCm39)	H142Q	probably damaging	Het
Slc27a3	G	A	3: 90,296,591 (GRCm39)	S127L		Het
Slc4a5	G	A	6: 83,239,466 (GRCm39)	A242T	probably benign	Het
Sphkap	G	A	1: 83,255,772 (GRCm39)	T659I	possibly damaging	Het
Ssbp3	T	C	4: 106,905,224 (GRCm39)	S381P	probably damaging	Het
Stxbp5l	C	T	16: 37,165,485 (GRCm39)	D78N	probably benign	Het
Suv39h2	G	T	2: 3,463,631 (GRCm39)	Q362K	probably benign	Het
Tcerg1	G	A	18: 42,701,030 (GRCm39)	R828Q	probably damaging	Het
Tgm2	T	G	2: 157,971,321 (GRCm39)	D306A	probably damaging	Het
Tmem79	A	G	3: 88,239,931 (GRCm39)	C260R	possibly damaging	Het
Ubn2	C	A	6: 38,466,190 (GRCm39)	A508E	probably benign	Het
Uggt2	T	A	14: 119,232,384 (GRCm39)	H1489L	possibly damaging	Het
Wnt16	T	C	6: 22,291,114 (GRCm39)	F181L	probably damaging	Het
Zfp326	T	C	5: 106,062,825 (GRCm39)	F565L	unknown	Het
Zfp62	T	A	11: 49,106,297 (GRCm39)	C129*	probably null	Het

Other mutations in Pcdha2

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL03052:Pcdha2	UTSW	18	37,074,670 (GRCm39)	missense	probably damaging	1.00
R3157:Pcdha2	UTSW	18	37,073,145 (GRCm39)	missense	probably damaging	1.00
R3159:Pcdha2	UTSW	18	37,074,250 (GRCm39)	missense	probably damaging	1.00
R3806:Pcdha2	UTSW	18	37,074,744 (GRCm39)	nonsense	probably null
R3806:Pcdha2	UTSW	18	37,072,582 (GRCm39)	missense	probably benign	0.02
R3815:Pcdha2	UTSW	18	37,074,748 (GRCm39)	missense	probably benign
R3816:Pcdha2	UTSW	18	37,074,748 (GRCm39)	missense	probably benign
R3937:Pcdha2	UTSW	18	37,074,376 (GRCm39)	missense	probably benign	0.42
R3970:Pcdha2	UTSW	18	37,073,750 (GRCm39)	nonsense	probably null
R4058:Pcdha2	UTSW	18	37,072,935 (GRCm39)	missense	probably benign	0.07
R4059:Pcdha2	UTSW	18	37,072,935 (GRCm39)	missense	probably benign	0.07
R4179:Pcdha2	UTSW	18	37,074,529 (GRCm39)	missense	probably damaging	1.00
R4457:Pcdha2	UTSW	18	37,073,599 (GRCm39)	missense	probably damaging	1.00
R4724:Pcdha2	UTSW	18	37,073,568 (GRCm39)	missense	possibly damaging	0.88
R4812:Pcdha2	UTSW	18	37,072,861 (GRCm39)	missense	probably benign
R4884:Pcdha2	UTSW	18	37,073,953 (GRCm39)	missense	probably damaging	1.00
R5130:Pcdha2	UTSW	18	37,073,722 (GRCm39)	missense	probably damaging	1.00
R5223:Pcdha2	UTSW	18	37,073,844 (GRCm39)	missense	probably damaging	1.00
R5442:Pcdha2	UTSW	18	37,072,915 (GRCm39)	missense	probably benign	0.14
R5460:Pcdha2	UTSW	18	37,072,474 (GRCm39)	missense	probably damaging	1.00
R5493:Pcdha2	UTSW	18	37,072,562 (GRCm39)	missense	probably damaging	0.98
R5946:Pcdha2	UTSW	18	37,074,159 (GRCm39)	missense	probably damaging	0.96
R6054:Pcdha2	UTSW	18	37,073,857 (GRCm39)	missense	probably damaging	1.00
R7378:Pcdha2	UTSW	18	37,072,438 (GRCm39)	missense	possibly damaging	0.88
R7465:Pcdha2	UTSW	18	37,073,383 (GRCm39)	missense	probably damaging	1.00
R7542:Pcdha2	UTSW	18	37,073,142 (GRCm39)	missense	probably damaging	0.99
R7774:Pcdha2	UTSW	18	37,074,579 (GRCm39)	missense	probably benign
R7953:Pcdha2	UTSW	18	37,072,579 (GRCm39)	missense	probably benign	0.00
R8043:Pcdha2	UTSW	18	37,072,579 (GRCm39)	missense	probably benign	0.00
R8048:Pcdha2	UTSW	18	37,072,513 (GRCm39)	missense	probably damaging	1.00
R8371:Pcdha2	UTSW	18	37,073,316 (GRCm39)	missense	possibly damaging	0.84
R8414:Pcdha2	UTSW	18	37,074,619 (GRCm39)	missense	probably damaging	1.00
R8472:Pcdha2	UTSW	18	37,074,325 (GRCm39)	missense	probably damaging	1.00
R8998:Pcdha2	UTSW	18	37,073,428 (GRCm39)	missense	possibly damaging	0.92
R8999:Pcdha2	UTSW	18	37,073,428 (GRCm39)	missense	possibly damaging	0.92
R9197:Pcdha2	UTSW	18	37,072,879 (GRCm39)	missense	probably damaging	1.00
R9462:Pcdha2	UTSW	18	37,073,546 (GRCm39)	missense	probably benign	0.07
Z1088:Pcdha2	UTSW	18	37,074,174 (GRCm39)	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- AGCTATGTGTCTGTGCATGC -3'
(R):5'- ATCCACTTCATCTAGGGCTCG -3'

Sequencing Primer
(F):5'- CAAGGTGTTCGCTCTGCAG -3'
(R):5'- CTTCATCTAGGGCTCGCGTGG -3'

Posted On

2022-11-14