Mutagenetix > Incidental Mutation

Incidental Mutation 'R5364:Pcdhb13'

423061

Institutional Source

Beutler Lab

Gene Symbol

Pcdhb13

Ensembl Gene

ENSMUSG00000047307

Gene Name

protocadherin beta 13

Synonyms

PcdhbM, Pcdbh6

MMRRC Submission

042942-MU

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.122) question?

Stock #

R5364 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

37575570-37579262 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 37576561 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Tyrosine to Cysteine at position 313 (Y313C)

Ref Sequence

ENSEMBL: ENSMUSP00000061087 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000052387] [ENSMUST00000055495] [ENSMUST00000056915] [ENSMUST00000115661] [ENSMUST00000194544]

AlphaFold

Q91Y06

Predicted Effect

probably benign
Transcript: ENSMUST00000052387

SMART Domains

Protein: ENSMUSP00000054111
Gene: ENSMUSG00000044043

Domain	Start	End	E-Value	Type
Pfam:Cadherin_2	30	112	1.4e-35	PFAM
CA	155	240	1.53e-20	SMART
CA	264	345	3.52e-29	SMART
CA	368	449	2.24e-22	SMART
CA	473	559	2.38e-26	SMART
CA	589	670	4.12e-12	SMART
Pfam:Cadherin_C_2	685	768	4.9e-27	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000055495

SMART Domains

Protein: ENSMUSP00000050357
Gene: ENSMUSG00000043458

Domain	Start	End	E-Value	Type
CA	53	130	1.67e-1	SMART
CA	154	239	3.69e-23	SMART
CA	263	343	6.56e-29	SMART
CA	366	447	5.9e-22	SMART
CA	471	557	4.24e-23	SMART
CA	587	668	1.01e-11	SMART
Pfam:Cadherin_C_2	685	768	4.8e-26	PFAM
low complexity region	778	790	N/A	INTRINSIC

Predicted Effect

probably damaging
Transcript: ENSMUST00000056915
AA Change: Y313C

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000061087
Gene: ENSMUSG00000047307
AA Change: Y313C

Domain	Start	End	E-Value	Type
signal peptide	1	28	N/A	INTRINSIC
CA	58	130	5.5e-1	SMART
CA	154	239	8.55e-19	SMART
CA	263	343	3.36e-26	SMART
CA	366	447	2.24e-22	SMART
CA	471	557	1.08e-24	SMART
CA	587	668	1.25e-11	SMART
Pfam:Cadherin_C_2	685	768	2.4e-23	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000115661

SMART Domains

Protein: ENSMUSP00000111325
Gene: ENSMUSG00000103458

Domain	Start	End	E-Value	Type
CA	20	131	5.3e-2	SMART
CA	155	240	1.51e-19	SMART
CA	264	348	7.6e-25	SMART
CA	372	453	1.42e-24	SMART
CA	477	563	1.42e-24	SMART
CA	594	674	4.12e-12	SMART
low complexity region	706	721	N/A	INTRINSIC
Pfam:Cadherin_tail	796	930	3.9e-58	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000193984

Predicted Effect

probably benign
Transcript: ENSMUST00000194544

SMART Domains

Protein: ENSMUSP00000141847
Gene: ENSMUSG00000102836

Domain	Start	End	E-Value	Type
Blast:CA	18	66	5e-20	BLAST

Meta Mutation Damage Score

0.7886

Coding Region Coverage

1x: 99.3%
3x: 98.8%
10x: 97.6%
20x: 96.3%

Validation Efficiency

100% (102/102)

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 beta gene cluster, one of three related gene clusters tandemly linked on chromosome five. The gene clusters demonstrate an unusual genomic organization similar to that of B-cell and T-cell receptor gene clusters. Unlike the alpha and gamma clusters, the transcripts from these genes do not share common 3' exons. 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 neural connections. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2014]

Allele List at MGI

Other mutations in this stock

Total: 91 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
2310022A10Rik	C	G	7: 27,278,192 (GRCm39)	T242R	probably damaging	Het
Abcc10	G	A	17: 46,616,577 (GRCm39)	R1205C	probably benign	Het
Acer1	A	G	17: 57,289,000 (GRCm39)	F37L	probably damaging	Het
Acp7	C	A	7: 28,310,448 (GRCm39)	G463V	probably benign	Het
Actr2	A	T	11: 20,050,797 (GRCm39)		probably benign	Het
Adam15	A	T	3: 89,252,902 (GRCm39)	I272K	probably damaging	Het
Adam1b	T	A	5: 121,638,946 (GRCm39)	I700F	possibly damaging	Het
Adam33	A	G	2: 130,896,392 (GRCm39)		probably null	Het
Ano1	T	C	7: 144,190,941 (GRCm39)	Y380C	probably damaging	Het
Arfgap3	A	C	15: 83,198,562 (GRCm39)	M307R	probably damaging	Het
Arhgap21	T	A	2: 20,854,533 (GRCm39)	R1610W	probably damaging	Het
Bbs2	A	G	8: 94,801,023 (GRCm39)	Y603H	probably benign	Het
Bbs9	G	T	9: 22,486,492 (GRCm39)		probably null	Het
Bcar3	A	C	3: 122,323,281 (GRCm39)	M779L	probably benign	Het
Bub3	A	T	7: 131,162,467 (GRCm39)	N10I	possibly damaging	Het
Cacna1c	T	G	6: 118,633,504 (GRCm39)	E1098D	probably benign	Het
Cacna1g	T	A	11: 94,307,684 (GRCm39)	M1738L	probably benign	Het
Camk2d	G	T	3: 126,574,069 (GRCm39)	G159C	probably damaging	Het
Ccdc51	A	T	9: 108,921,188 (GRCm39)	E358D	possibly damaging	Het
Cdc42bpa	A	G	1: 179,894,747 (GRCm39)	D309G	probably benign	Het
Cdhr3	A	T	12: 33,101,007 (GRCm39)	F468I	possibly damaging	Het
Chrd	A	G	16: 20,551,898 (GRCm39)	M1V	probably null	Het
Cmtm1	CGGCACGTACTGAAGGTCGCTGACTGGATGGTGTGGCACGTACTGAAGGTCGCTGACTGGATGGTGTGGCACGTACTGAAGGTCGCTGACTGGATGGT	CGGCACGTACTGAAGGTCGCTGACTGGATGGTGTGGCACGTACTGAAGGTCGCTGACTGGATGGT	8: 105,036,102 (GRCm39)		probably benign	Het
Dcdc2b	T	C	4: 129,502,963 (GRCm39)	Y253C	probably damaging	Het
Dclk1	A	C	3: 55,163,366 (GRCm39)	N153H	possibly damaging	Het
Dgkg	G	T	16: 22,419,211 (GRCm39)	S96R	probably benign	Het
Dnah9	A	G	11: 65,772,522 (GRCm39)	Y3737H	possibly damaging	Het
Elovl4	A	T	9: 83,672,076 (GRCm39)	I81N	probably benign	Het
Epha7	T	A	4: 28,950,557 (GRCm39)	Y791N	probably damaging	Het
Fam193a	C	A	5: 34,623,597 (GRCm39)	T1395N	probably benign	Het
Fbln5	A	T	12: 101,737,623 (GRCm39)	V141E	probably damaging	Het
Flii	T	C	11: 60,610,954 (GRCm39)	T492A	probably benign	Het
Fnip2	A	G	3: 79,388,475 (GRCm39)	I752T	probably benign	Het
Fpr3	T	C	17: 18,190,806 (GRCm39)	W26R	probably benign	Het
Gabrb1	A	T	5: 72,294,105 (GRCm39)	T460S	probably benign	Het
Gde1	T	C	7: 118,297,874 (GRCm39)	N4S	probably benign	Het
Ghitm	G	T	14: 36,847,156 (GRCm39)	T306K	probably benign	Het
Ghitm	A	T	14: 36,847,174 (GRCm39)	I300N	probably damaging	Het
Gm4787	G	C	12: 81,424,604 (GRCm39)	T518S	probably benign	Het
Iqcd	T	C	5: 120,738,332 (GRCm39)	I50T	probably damaging	Het
Itpripl1	G	A	2: 126,983,739 (GRCm39)	P128S	possibly damaging	Het
Jag2	C	A	12: 112,874,154 (GRCm39)	L1000F	probably damaging	Het
Klhdc4	A	T	8: 122,533,375 (GRCm39)		probably benign	Het
Klra5	A	G	6: 129,876,316 (GRCm39)	F164L	probably benign	Het
Larp1b	A	G	3: 40,931,658 (GRCm39)	Y288C	probably damaging	Het
Lrfn3	T	A	7: 30,055,078 (GRCm39)	E622D	possibly damaging	Het
Lyst	A	G	13: 13,831,439 (GRCm39)	D1621G	probably benign	Het
Mastl	T	C	2: 23,023,665 (GRCm39)	T353A	probably benign	Het
Mkln1	T	C	6: 31,473,647 (GRCm39)	Y130H	probably damaging	Het
Mms22l	T	A	4: 24,496,882 (GRCm39)		probably benign	Het
Mroh7	T	A	4: 106,548,840 (GRCm39)	M1008L	probably benign	Het
Nipal1	T	C	5: 72,825,243 (GRCm39)	V312A	probably damaging	Het
Nlrp5	T	A	7: 23,117,753 (GRCm39)	Y492*	probably null	Het
Odad1	T	A	7: 45,585,756 (GRCm39)	I105N	probably damaging	Het
Or1n1	T	C	2: 36,750,006 (GRCm39)	Y118C	probably damaging	Het
Otulinl	G	A	15: 27,660,031 (GRCm39)	Q24*	probably null	Het
Pcdhb11	T	A	18: 37,555,232 (GRCm39)	D187E	probably benign	Het
Pdpn	G	A	4: 143,000,526 (GRCm39)	T102I	possibly damaging	Het
Pear1	A	T	3: 87,665,668 (GRCm39)	C120S	probably damaging	Het
Peg10	T	C	6: 4,756,128 (GRCm39)		probably benign	Het
Ppm1e	A	G	11: 87,128,007 (GRCm39)	W384R	probably benign	Het
Ppp1r10	C	T	17: 36,241,324 (GRCm39)	P700S	unknown	Het
Prl2c5	G	A	13: 13,357,627 (GRCm39)	R13K	probably benign	Het
Prmt3	C	A	7: 49,498,554 (GRCm39)	P487T	probably damaging	Het
Proser3	C	A	7: 30,245,573 (GRCm39)	A144S	possibly damaging	Het
Ptcd1	G	A	5: 145,088,241 (GRCm39)	T590I	probably damaging	Het
Rbsn	A	G	6: 92,170,958 (GRCm39)	V321A	probably damaging	Het
Slc40a1	C	A	1: 45,964,383 (GRCm39)	C14F	probably damaging	Het
Slc6a15	T	C	10: 103,229,369 (GRCm39)	I136T	probably damaging	Het
Slc7a4	A	G	16: 17,391,227 (GRCm39)	I449T	probably benign	Het
Snrnp48	T	A	13: 38,394,165 (GRCm39)		probably null	Het
Tada2a	A	G	11: 84,011,973 (GRCm39)	Y23H	probably benign	Het
Tbx15	A	T	3: 99,259,508 (GRCm39)	S460C	possibly damaging	Het
Tbx21	C	T	11: 96,992,304 (GRCm39)		probably null	Het
Tmcc2	T	G	1: 132,285,534 (GRCm39)	T376P	probably damaging	Het
Tmco4	G	A	4: 138,779,815 (GRCm39)	C420Y	probably damaging	Het
Tmem235	C	A	11: 117,755,020 (GRCm39)	Y157*	probably null	Het
Tmem63b	T	C	17: 45,975,653 (GRCm39)		probably benign	Het
Tnfrsf1a	T	C	6: 125,334,356 (GRCm39)	S92P	possibly damaging	Het
Top3b	A	T	16: 16,704,834 (GRCm39)	T397S	probably benign	Het
Trabd	C	A	15: 88,967,007 (GRCm39)		probably benign	Het
Trbv21	A	T	6: 41,179,764 (GRCm39)	I27L	possibly damaging	Het
Trim3	C	T	7: 105,268,276 (GRCm39)	V169M	probably damaging	Het
Ttn	T	C	2: 76,807,458 (GRCm39)	T92A	probably damaging	Het
Ttn	C	T	2: 76,738,860 (GRCm39)	S3893N	probably benign	Het
Uchl4	A	T	9: 64,142,821 (GRCm39)	I101F	possibly damaging	Het
Vmn1r5	T	A	6: 56,962,583 (GRCm39)	M86K	probably damaging	Het
Vmn2r55	T	A	7: 12,404,830 (GRCm39)	Q191L	possibly damaging	Het
Zfp458	A	T	13: 67,406,012 (GRCm39)	C139*	probably null	Het
Zfp788	T	C	7: 41,299,551 (GRCm39)	L729P	probably damaging	Het
Zmym2	T	A	14: 57,158,102 (GRCm39)	M547K	possibly damaging	Het

Other mutations in Pcdhb13

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00654:Pcdhb13	APN	18	37,576,774 (GRCm39)	missense	possibly damaging	0.56
IGL00718:Pcdhb13	APN	18	37,577,874 (GRCm39)	missense	possibly damaging	0.91
IGL01143:Pcdhb13	APN	18	37,575,690 (GRCm39)	missense	probably benign	0.01
IGL01816:Pcdhb13	APN	18	37,576,028 (GRCm39)	missense	probably benign	0.00
IGL01916:Pcdhb13	APN	18	37,576,914 (GRCm39)	missense	possibly damaging	0.64
IGL02063:Pcdhb13	APN	18	37,577,282 (GRCm39)	missense	probably damaging	1.00
IGL02153:Pcdhb13	APN	18	37,576,738 (GRCm39)	missense	probably damaging	1.00
IGL02332:Pcdhb13	APN	18	37,576,635 (GRCm39)	missense	probably benign	0.32
IGL02407:Pcdhb13	APN	18	37,576,128 (GRCm39)	missense	probably damaging	1.00
IGL02423:Pcdhb13	APN	18	37,577,392 (GRCm39)	missense	possibly damaging	0.95
IGL02514:Pcdhb13	APN	18	37,576,044 (GRCm39)	missense	possibly damaging	0.80
IGL03025:Pcdhb13	APN	18	37,575,817 (GRCm39)	missense	probably damaging	1.00
IGL03227:Pcdhb13	APN	18	37,576,711 (GRCm39)	missense	probably damaging	0.98
IGL03233:Pcdhb13	APN	18	37,577,318 (GRCm39)	missense	probably damaging	0.96
IGL03239:Pcdhb13	APN	18	37,575,888 (GRCm39)	missense	probably damaging	0.97
R0046:Pcdhb13	UTSW	18	37,577,310 (GRCm39)	missense	probably benign
R0172:Pcdhb13	UTSW	18	37,575,990 (GRCm39)	missense	probably benign	0.00
R0201:Pcdhb13	UTSW	18	37,575,634 (GRCm39)	missense	probably benign
R0594:Pcdhb13	UTSW	18	37,576,984 (GRCm39)	missense	probably damaging	1.00
R1235:Pcdhb13	UTSW	18	37,578,012 (GRCm39)	makesense	probably null
R1292:Pcdhb13	UTSW	18	37,576,885 (GRCm39)	missense	probably benign	0.43
R1481:Pcdhb13	UTSW	18	37,575,889 (GRCm39)	missense	probably damaging	1.00
R1991:Pcdhb13	UTSW	18	37,576,912 (GRCm39)	missense	possibly damaging	0.80
R2058:Pcdhb13	UTSW	18	37,577,620 (GRCm39)	missense	possibly damaging	0.95
R3508:Pcdhb13	UTSW	18	37,576,204 (GRCm39)	missense	probably damaging	0.99
R3713:Pcdhb13	UTSW	18	37,576,786 (GRCm39)	missense	probably damaging	1.00
R4125:Pcdhb13	UTSW	18	37,576,873 (GRCm39)	missense	probably damaging	1.00
R4741:Pcdhb13	UTSW	18	37,576,571 (GRCm39)	missense	probably benign	0.01
R4747:Pcdhb13	UTSW	18	37,577,868 (GRCm39)	missense	probably damaging	0.99
R4957:Pcdhb13	UTSW	18	37,577,837 (GRCm39)	missense	possibly damaging	0.95
R4973:Pcdhb13	UTSW	18	37,576,237 (GRCm39)	missense	probably benign	0.20
R5354:Pcdhb13	UTSW	18	37,577,844 (GRCm39)	missense	probably damaging	1.00
R5544:Pcdhb13	UTSW	18	37,576,573 (GRCm39)	missense	possibly damaging	0.92
R5897:Pcdhb13	UTSW	18	37,576,264 (GRCm39)	missense	probably benign	0.42
R6174:Pcdhb13	UTSW	18	37,576,474 (GRCm39)	missense	possibly damaging	0.84
R6702:Pcdhb13	UTSW	18	37,577,828 (GRCm39)	missense	probably benign	0.42
R6765:Pcdhb13	UTSW	18	37,576,663 (GRCm39)	missense	probably damaging	1.00
R6960:Pcdhb13	UTSW	18	37,576,509 (GRCm39)	missense	probably benign	0.45
R7144:Pcdhb13	UTSW	18	37,576,309 (GRCm39)	missense	probably damaging	1.00
R7225:Pcdhb13	UTSW	18	37,577,490 (GRCm39)	missense	possibly damaging	0.91
R7239:Pcdhb13	UTSW	18	37,577,697 (GRCm39)	missense	probably damaging	0.99
R7437:Pcdhb13	UTSW	18	37,577,728 (GRCm39)	missense	probably damaging	1.00
R7812:Pcdhb13	UTSW	18	37,575,645 (GRCm39)	missense	probably benign	0.00
R7964:Pcdhb13	UTSW	18	37,577,871 (GRCm39)	missense	possibly damaging	0.62
R8334:Pcdhb13	UTSW	18	37,577,853 (GRCm39)	missense	probably damaging	1.00
R8463:Pcdhb13	UTSW	18	37,576,287 (GRCm39)	missense	possibly damaging	0.94
R8476:Pcdhb13	UTSW	18	37,577,137 (GRCm39)	missense	probably damaging	1.00
R8501:Pcdhb13	UTSW	18	37,577,493 (GRCm39)	missense	probably damaging	1.00
R9248:Pcdhb13	UTSW	18	37,577,608 (GRCm39)	missense	probably damaging	1.00
R9569:Pcdhb13	UTSW	18	37,576,153 (GRCm39)	missense	probably damaging	1.00
X0023:Pcdhb13	UTSW	18	37,576,066 (GRCm39)	missense	probably damaging	1.00
X0028:Pcdhb13	UTSW	18	37,577,695 (GRCm39)	missense	possibly damaging	0.91
Z1176:Pcdhb13	UTSW	18	37,576,288 (GRCm39)	nonsense	probably null
Z1177:Pcdhb13	UTSW	18	37,575,633 (GRCm39)	missense	probably benign	0.00

Predicted Primers

PCR Primer
(F):5'- AGCTCTATGAGGTCCAAGTTCC -3'
(R):5'- TGGTTATTTCCAGAGTCCGCATC -3'

Sequencing Primer
(F):5'- TGAGAACAGTCCCATTGGCTC -3'
(R):5'- TATTTCCAGAGTCCGCATCTGAAAC -3'

Posted On

2016-08-04