Mutagenetix > Incidental Mutation

Incidental Mutation 'R9667:Pcdhb20'

727895

Institutional Source

Beutler Lab

Gene Symbol

Pcdhb20

Ensembl Gene

ENSMUSG00000046191

Gene Name

protocadherin beta 20

Synonyms

Pcdhb14, PcdhbT

MMRRC Submission

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.083) question?

Stock #

R9667 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

37637332-37640713 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

C to T at 37637839 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Histidine to Tyrosine at position 122 (H122Y)

Ref Sequence

ENSEMBL: ENSMUSP00000137038 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000052179] [ENSMUST00000059571] [ENSMUST00000115661] [ENSMUST00000194544]

AlphaFold

Q91XZ9

Predicted Effect

probably benign
Transcript: ENSMUST00000052179
AA Change: H122Y

PolyPhen 2 Score 0.004 (Sensitivity: 0.98; Specificity: 0.59)

SMART Domains

Protein: ENSMUSP00000137038
Gene: ENSMUSG00000046191
AA Change: H122Y

Domain	Start	End	E-Value	Type
Pfam:Cadherin_2	30	112	8.3e-36	PFAM
low complexity region	136	148	N/A	INTRINSIC
CA	155	240	1.41e-19	SMART
CA	264	345	2.91e-21	SMART
CA	368	449	1.12e-22	SMART
CA	473	559	3.41e-27	SMART
CA	589	670	6.34e-13	SMART
Pfam:Cadherin_C_2	686	769	7.1e-26	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000059571

SMART Domains

Protein: ENSMUSP00000053326
Gene: ENSMUSG00000043313

Domain	Start	End	E-Value	Type
signal peptide	1	26	N/A	INTRINSIC
CA	45	131	4.8e-1	SMART
CA	155	240	6.58e-20	SMART
CA	264	345	1.03e-21	SMART
CA	368	449	4.21e-18	SMART
CA	473	559	3.36e-26	SMART
CA	589	670	6.69e-12	SMART
Pfam:Cadherin_C_2	686	769	1.9e-25	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

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.7%
20x: 98.8%

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 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. The beta cluster contains 16 genes and 3 pseudogenes, each encoding 6 extracellular cadherin domains and a cytoplasmic tail that deviates from others in the cadherin superfamily. The extracellular domains interact in a homophilic manner to specify differential cell-cell connections. Unlike the alpha and gamma clusters, the transcripts from these genes are made up of only one large exon, not sharing common 3' exons as expected. These neural cadherin-like cell adhesion proteins are integral plasma membrane proteins. Their specific functions are unknown but they most likely play a critical role in the establishment and function of specific cell-cell neural connections. [provided by RefSeq, Jul 2008]

Allele List at MGI

Other mutations in this stock

Total: 88 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4930563M21Rik	G	A	9: 55,890,645 (GRCm39)	Q355*	probably null	Het
Aacs	A	T	5: 125,580,691 (GRCm39)	N255I	possibly damaging	Het
Abcf2	A	G	5: 24,779,185 (GRCm39)	L121P	probably damaging	Het
Amigo1	A	G	3: 108,095,034 (GRCm39)	I178V	probably benign	Het
Ankrd13a	T	A	5: 114,933,793 (GRCm39)	N262K	probably damaging	Het
Apba2	A	G	7: 64,345,062 (GRCm39)	E84G	possibly damaging	Het
Arhgap35	A	T	7: 16,296,914 (GRCm39)	L717*	probably null	Het
Aspa	A	T	11: 73,199,625 (GRCm39)	C217*	probably null	Het
Atp5mc3	A	G	2: 73,739,567 (GRCm39)	I91T	probably damaging	Het
Birc6	T	C	17: 75,004,420 (GRCm39)	M4763T	possibly damaging	Het
Cc2d2b	A	G	19: 40,753,927 (GRCm39)	Y150C	unknown	Het
Ccdc180	C	T	4: 45,920,861 (GRCm39)	Q936*	probably null	Het
Cdc42bpg	A	G	19: 6,370,115 (GRCm39)	E1103G	probably benign	Het
Cdca2	T	C	14: 67,915,003 (GRCm39)	Q752R	probably benign	Het
Ces1b	A	T	8: 93,791,637 (GRCm39)	S321T	probably benign	Het
Cfap70	A	T	14: 20,490,690 (GRCm39)		probably null	Het
Cpox	C	T	16: 58,490,984 (GRCm39)	T65I	possibly damaging	Het
Crocc	C	T	4: 140,748,988 (GRCm39)	E1606K	probably damaging	Het
Cryzl2	T	G	1: 157,316,038 (GRCm39)	M337R	probably benign	Het
Cyp4a29	C	A	4: 115,111,630 (GRCm39)	A469D	probably damaging	Het
Dnaaf1	T	A	8: 120,306,043 (GRCm39)	Y107N	possibly damaging	Het
Dpp6	T	A	5: 27,930,604 (GRCm39)	I812N	probably damaging	Het
Elovl5	A	G	9: 77,889,947 (GRCm39)	T253A	possibly damaging	Het
Fancd2	T	A	6: 113,530,717 (GRCm39)	L450*	probably null	Het
Fbxo31	C	T	8: 122,305,208 (GRCm39)	R96H	probably damaging	Het
Gls	A	T	1: 52,230,036 (GRCm39)		probably null	Het
Gm3045	G	A	13: 56,577,253 (GRCm39)	E134K	possibly damaging	Het
Gpr158	A	G	2: 21,830,054 (GRCm39)	I700V	probably damaging	Het
H2-Aa	T	C	17: 34,502,295 (GRCm39)	I209V	probably benign	Het
Ifnar2	A	G	16: 91,184,984 (GRCm39)	D125G	probably benign	Het
Igsf8	C	A	1: 172,145,319 (GRCm39)	D278E	possibly damaging	Het
Inpp5d	T	C	1: 87,623,128 (GRCm39)	I407T	probably damaging	Het
Iqcd	A	G	5: 120,744,737 (GRCm39)	E355G	probably damaging	Het
Klra2	T	A	6: 131,219,836 (GRCm39)	D115V	probably benign	Het
Kmt2b	T	C	7: 30,287,784 (GRCm39)	E120G	unknown	Het
Lhx6	A	G	2: 35,980,979 (GRCm39)	I321T	possibly damaging	Het
Lmna	CAGCACGGTGCGTGAGC	CAGC	3: 88,389,857 (GRCm39)		probably null	Het
Lztr1	T	C	16: 17,327,000 (GRCm39)	Y37H	probably damaging	Het
Malrd1	A	T	2: 15,570,026 (GRCm39)		probably null	Het
Mtmr3	C	T	11: 4,470,890 (GRCm39)	V79I	probably damaging	Het
Nbr1	A	G	11: 101,451,261 (GRCm39)	I56M	possibly damaging	Het
Ncor2	C	T	5: 125,125,545 (GRCm39)	A580T	unknown	Het
Ndst3	A	G	3: 123,353,866 (GRCm39)	I601T	possibly damaging	Het
Nectin4	C	A	1: 171,210,165 (GRCm39)	P219Q	probably damaging	Het
Nfatc4	T	C	14: 56,066,964 (GRCm39)	V501A	probably benign	Het
Nisch	T	C	14: 30,895,646 (GRCm39)	T1015A	probably damaging	Het
Nr2c1	T	C	10: 94,017,479 (GRCm39)		probably null	Het
Nrg2	T	C	18: 36,165,430 (GRCm39)	E394G	probably benign	Het
Oas1e	A	G	5: 120,932,347 (GRCm39)	F99L	probably benign	Het
Oaz3	A	T	3: 94,341,835 (GRCm39)	Y178*	probably null	Het
Or1e35	A	G	11: 73,798,097 (GRCm39)	S74P	possibly damaging	Het
Or6c69b	A	C	10: 129,627,022 (GRCm39)	S145R	probably damaging	Het
Pdcd2	T	A	17: 15,747,535 (GRCm39)	M1L	probably damaging	Het
Phf11	T	C	14: 59,482,240 (GRCm39)	N171S	probably benign	Het
Plcd1	C	A	9: 118,901,698 (GRCm39)	G609W	probably damaging	Het
Plscr3	T	C	11: 69,738,631 (GRCm39)	F98L	probably benign	Het
Ppp1r8	T	C	4: 132,570,407 (GRCm39)	N6S	probably benign	Het
Prpf38b	G	A	3: 108,818,859 (GRCm39)		probably benign	Het
Rin2	T	A	2: 145,702,202 (GRCm39)	N299K	possibly damaging	Het
Serpina1d	T	G	12: 103,734,299 (GRCm39)	T2P	probably benign	Het
Slc22a16	A	G	10: 40,461,125 (GRCm39)	D330G	probably benign	Het
Slit1	G	A	19: 41,731,832 (GRCm39)	Q6*	probably null	Het
Spaca7b	T	A	8: 11,705,681 (GRCm39)	E142V	probably benign	Het
Spag9	T	C	11: 93,887,119 (GRCm39)	V8A	possibly damaging	Het
Spsb3	C	T	17: 25,105,784 (GRCm39)	T44I	unknown	Het
Srrt	T	C	5: 137,295,732 (GRCm39)	Y563C	probably damaging	Het
Syne2	A	G	12: 75,926,951 (GRCm39)	D69G	probably damaging	Het
Tcf12	A	G	9: 71,792,443 (GRCm39)	V80A	probably benign	Het
Tdpoz3	G	A	3: 93,733,336 (GRCm39)	D4N	possibly damaging	Het
Tekt2	C	T	4: 126,217,444 (GRCm39)	R207H	probably damaging	Het
Tmem132d	G	A	5: 128,061,375 (GRCm39)	T409I	possibly damaging	Het
Tmem245	G	T	4: 56,947,119 (GRCm39)	T98K	probably damaging	Het
Tmem70	A	C	1: 16,735,659 (GRCm39)	E43A	probably benign	Het
Trim25	A	T	11: 88,907,188 (GRCm39)	I516F	probably damaging	Het
Trim3	G	A	7: 105,267,455 (GRCm39)	S308L	possibly damaging	Het
Ttll9	C	T	2: 152,831,989 (GRCm39)	R189*	probably null	Het
Ttpal	T	C	2: 163,449,596 (GRCm39)		probably null	Het
Ubl4b	A	T	3: 107,461,911 (GRCm39)	H116Q	probably benign	Het
Unc80	C	A	1: 66,651,287 (GRCm39)	T1544K	possibly damaging	Het
Usp2	T	C	9: 44,003,487 (GRCm39)		probably null	Het
Usp25	T	C	16: 76,874,123 (GRCm39)		probably null	Het
Vmn1r167	C	T	7: 23,204,990 (GRCm39)	V9I	probably benign	Het
Vmn2r87	A	G	10: 130,314,776 (GRCm39)	I270T	probably damaging	Het
Vps35l	G	A	7: 118,348,915 (GRCm39)		probably null	Het
Wdr24	A	G	17: 26,046,301 (GRCm39)	D515G	possibly damaging	Het
Wdr81	T	C	11: 75,341,650 (GRCm39)	T87A		Het
Zcchc14	A	T	8: 122,331,863 (GRCm39)	L500Q	unknown	Het
Zzef1	A	G	11: 72,758,786 (GRCm39)	T1242A	probably benign	Het

Other mutations in Pcdhb20

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01071:Pcdhb20	APN	18	37,637,738 (GRCm39)	missense	possibly damaging	0.87
IGL01373:Pcdhb20	APN	18	37,639,621 (GRCm39)	missense	probably benign	0.10
IGL01556:Pcdhb20	APN	18	37,637,852 (GRCm39)	missense	possibly damaging	0.88
IGL01621:Pcdhb20	APN	18	37,637,860 (GRCm39)	missense	possibly damaging	0.49
IGL01768:Pcdhb20	APN	18	37,639,768 (GRCm39)	missense	possibly damaging	0.80
IGL01859:Pcdhb20	APN	18	37,637,616 (GRCm39)	missense	probably damaging	0.98
IGL02492:Pcdhb20	APN	18	37,639,453 (GRCm39)	missense	probably benign	0.43
IGL03057:Pcdhb20	APN	18	37,637,851 (GRCm39)	missense	possibly damaging	0.74
IGL02991:Pcdhb20	UTSW	18	37,639,264 (GRCm39)	missense	probably damaging	1.00
R0799:Pcdhb20	UTSW	18	37,638,938 (GRCm39)	missense	probably damaging	1.00
R1465:Pcdhb20	UTSW	18	37,637,750 (GRCm39)	missense	probably damaging	0.99
R1465:Pcdhb20	UTSW	18	37,637,750 (GRCm39)	missense	probably damaging	0.99
R2012:Pcdhb20	UTSW	18	37,638,127 (GRCm39)	missense	probably damaging	0.99
R2079:Pcdhb20	UTSW	18	37,638,224 (GRCm39)	missense	probably benign	0.07
R2350:Pcdhb20	UTSW	18	37,637,563 (GRCm39)	missense	probably benign	0.01
R2363:Pcdhb20	UTSW	18	37,638,725 (GRCm39)	missense	probably damaging	1.00
R2364:Pcdhb20	UTSW	18	37,638,991 (GRCm39)	missense	probably damaging	1.00
R2870:Pcdhb20	UTSW	18	37,638,833 (GRCm39)	missense	possibly damaging	0.82
R2870:Pcdhb20	UTSW	18	37,638,833 (GRCm39)	missense	possibly damaging	0.82
R4060:Pcdhb20	UTSW	18	37,639,217 (GRCm39)	missense	probably damaging	1.00
R4609:Pcdhb20	UTSW	18	37,638,849 (GRCm39)	missense	probably benign	0.02
R4750:Pcdhb20	UTSW	18	37,639,184 (GRCm39)	missense	possibly damaging	0.48
R4897:Pcdhb20	UTSW	18	37,639,298 (GRCm39)	missense	possibly damaging	0.70
R4970:Pcdhb20	UTSW	18	37,639,824 (GRCm39)	missense	probably benign	0.00
R5098:Pcdhb20	UTSW	18	37,637,858 (GRCm39)	missense	probably damaging	1.00
R5616:Pcdhb20	UTSW	18	37,637,585 (GRCm39)	missense	probably damaging	0.97
R5890:Pcdhb20	UTSW	18	37,638,286 (GRCm39)	missense	probably benign	0.00
R6225:Pcdhb20	UTSW	18	37,638,047 (GRCm39)	missense	probably damaging	1.00
R6248:Pcdhb20	UTSW	18	37,639,285 (GRCm39)	missense	probably damaging	0.99
R6419:Pcdhb20	UTSW	18	37,638,608 (GRCm39)	missense	probably damaging	1.00
R6814:Pcdhb20	UTSW	18	37,639,218 (GRCm39)	missense	probably benign	0.22
R6821:Pcdhb20	UTSW	18	37,639,175 (GRCm39)	missense	probably damaging	1.00
R6824:Pcdhb20	UTSW	18	37,638,752 (GRCm39)	missense	probably benign	0.06
R6872:Pcdhb20	UTSW	18	37,639,218 (GRCm39)	missense	probably benign	0.22
R7040:Pcdhb20	UTSW	18	37,637,770 (GRCm39)	missense	probably benign	0.00
R7145:Pcdhb20	UTSW	18	37,638,142 (GRCm39)	missense	probably damaging	1.00
R7165:Pcdhb20	UTSW	18	37,638,123 (GRCm39)	missense	probably damaging	1.00
R7215:Pcdhb20	UTSW	18	37,638,439 (GRCm39)	missense	probably benign	0.24
R7265:Pcdhb20	UTSW	18	37,638,616 (GRCm39)	missense	possibly damaging	0.95
R7372:Pcdhb20	UTSW	18	37,639,840 (GRCm39)	missense	probably benign	0.00
R7402:Pcdhb20	UTSW	18	37,638,005 (GRCm39)	missense	probably benign	0.05
R7718:Pcdhb20	UTSW	18	37,638,704 (GRCm39)	missense	probably damaging	1.00
R7794:Pcdhb20	UTSW	18	37,637,485 (GRCm39)	missense	probably benign	0.00
R7842:Pcdhb20	UTSW	18	37,638,112 (GRCm39)	missense	possibly damaging	0.94
R8084:Pcdhb20	UTSW	18	37,639,226 (GRCm39)	missense	possibly damaging	0.95
R8133:Pcdhb20	UTSW	18	37,639,663 (GRCm39)	nonsense	probably null
R8422:Pcdhb20	UTSW	18	37,637,849 (GRCm39)	missense	probably damaging	1.00
R8477:Pcdhb20	UTSW	18	37,638,307 (GRCm39)	missense	probably benign	0.12
R8727:Pcdhb20	UTSW	18	37,638,437 (GRCm39)	missense	probably damaging	1.00
R8733:Pcdhb20	UTSW	18	37,638,437 (GRCm39)	missense	probably damaging	1.00
R8951:Pcdhb20	UTSW	18	37,639,146 (GRCm39)	missense	probably damaging	1.00
R9196:Pcdhb20	UTSW	18	37,638,024 (GRCm39)	missense	probably benign	0.00
R9384:Pcdhb20	UTSW	18	37,638,024 (GRCm39)	missense	probably benign	0.00
R9388:Pcdhb20	UTSW	18	37,638,853 (GRCm39)	missense	probably benign	0.02
R9462:Pcdhb20	UTSW	18	37,639,799 (GRCm39)	missense	probably benign	0.30
Z1177:Pcdhb20	UTSW	18	37,637,641 (GRCm39)	missense	possibly damaging	0.95

Predicted Primers

PCR Primer
(F):5'- TCTGGCAAAGGATTTAGGACTGG -3'
(R):5'- TTTGTCCAGAACCAGCTCCG -3'

Sequencing Primer
(F):5'- AGCTGTCCTCCAGGGAG -3'
(R):5'- GAACCAGCTCCGGGTATATC -3'

Posted On

2022-10-06