Mutagenetix > Incidental Mutation

Incidental Mutation 'R8876:Xndc1'

676574

Institutional Source

Beutler Lab

Gene Symbol

Xndc1

Ensembl Gene

ENSMUSG00000099481

Gene Name

Xrcc1 N-terminal domain containing 1

Synonyms

Xndr

MMRRC Submission

068688-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R8876 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

101714718-101732972 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

C to T at 101729754 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Proline to Leucine at position 267 (P267L)

Ref Sequence

ENSEMBL: ENSMUSP00000091680 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000084843] [ENSMUST00000094130] [ENSMUST00000106950] [ENSMUST00000123372] [ENSMUST00000124189] [ENSMUST00000139104] [ENSMUST00000142629] [ENSMUST00000146450]

AlphaFold

no structure available at present

Predicted Effect

probably benign
Transcript: ENSMUST00000084843
AA Change: P267L

PolyPhen 2 Score 0.091 (Sensitivity: 0.93; Specificity: 0.85)

SMART Domains

Protein: ENSMUSP00000081903
Gene: ENSMUSG00000070425
AA Change: P267L

Domain	Start	End	E-Value	Type
Pfam:XRCC1_N	1	150	1.4e-54	PFAM
low complexity region	254	267	N/A	INTRINSIC
low complexity region	275	280	N/A	INTRINSIC
low complexity region	297	311	N/A	INTRINSIC
low complexity region	345	362	N/A	INTRINSIC
low complexity region	403	415	N/A	INTRINSIC
low complexity region	416	428	N/A	INTRINSIC
ANK	439	469	1.58e3	SMART
low complexity region	484	496	N/A	INTRINSIC
ANK	522	551	1.74e0	SMART
Pfam:TRP_2	557	619	1e-24	PFAM
Pfam:Ion_trans	716	1024	1.7e-24	PFAM
Pfam:PKD_channel	774	1019	2.4e-12	PFAM
low complexity region	1070	1081	N/A	INTRINSIC
low complexity region	1093	1104	N/A	INTRINSIC
coiled coil region	1122	1162	N/A	INTRINSIC
low complexity region	1220	1236	N/A	INTRINSIC
low complexity region	1247	1263	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000094130
AA Change: P267L

PolyPhen 2 Score 0.065 (Sensitivity: 0.94; Specificity: 0.84)

SMART Domains

Protein: ENSMUSP00000091680
Gene: ENSMUSG00000099481
AA Change: P267L

Domain	Start	End	E-Value	Type
Pfam:XRCC1_N	1	152	5.2e-29	PFAM
low complexity region	254	267	N/A	INTRINSIC
low complexity region	275	280	N/A	INTRINSIC
low complexity region	297	311	N/A	INTRINSIC
internal_repeat_1	324	345	2.69e-6	PROSPERO
low complexity region	346	379	N/A	INTRINSIC
internal_repeat_1	380	401	2.69e-6	PROSPERO

Predicted Effect

probably benign
Transcript: ENSMUST00000106950
AA Change: P267L

PolyPhen 2 Score 0.065 (Sensitivity: 0.94; Specificity: 0.84)

SMART Domains

Protein: ENSMUSP00000102563
Gene: ENSMUSG00000099481
AA Change: P267L

Domain	Start	End	E-Value	Type
Pfam:XRCC1_N	1	152	5.2e-29	PFAM
low complexity region	254	267	N/A	INTRINSIC
low complexity region	275	280	N/A	INTRINSIC
low complexity region	297	311	N/A	INTRINSIC
internal_repeat_1	324	345	2.69e-6	PROSPERO
low complexity region	346	379	N/A	INTRINSIC
internal_repeat_1	380	401	2.69e-6	PROSPERO

Predicted Effect

probably benign
Transcript: ENSMUST00000123372
AA Change: P267L

PolyPhen 2 Score 0.065 (Sensitivity: 0.94; Specificity: 0.84)

SMART Domains

Protein: ENSMUSP00000121068
Gene: ENSMUSG00000070425
AA Change: P267L

Domain	Start	End	E-Value	Type
Pfam:XRCC1_N	1	152	5.2e-29	PFAM
low complexity region	254	267	N/A	INTRINSIC
low complexity region	275	280	N/A	INTRINSIC
low complexity region	297	311	N/A	INTRINSIC
internal_repeat_1	324	345	2.69e-6	PROSPERO
low complexity region	346	379	N/A	INTRINSIC
internal_repeat_1	380	401	2.69e-6	PROSPERO

Predicted Effect

probably benign
Transcript: ENSMUST00000124189

SMART Domains

Protein: ENSMUSP00000116934
Gene: ENSMUSG00000100254

Domain	Start	End	E-Value	Type
low complexity region	29	41	N/A	INTRINSIC
low complexity region	42	54	N/A	INTRINSIC
ANK	65	95	1.58e3	SMART
low complexity region	110	122	N/A	INTRINSIC
ANK	148	177	1.74e0	SMART
Pfam:TRP_2	183	245	9.1e-29	PFAM
transmembrane domain	345	367	N/A	INTRINSIC
Pfam:PKD_channel	398	645	1.4e-12	PFAM
Pfam:Ion_trans	422	638	1e-31	PFAM
low complexity region	696	707	N/A	INTRINSIC
low complexity region	719	730	N/A	INTRINSIC
coiled coil region	748	788	N/A	INTRINSIC
low complexity region	846	862	N/A	INTRINSIC
low complexity region	873	889	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000139104

SMART Domains

Protein: ENSMUSP00000122430
Gene: ENSMUSG00000070425

Domain	Start	End	E-Value	Type
Pfam:XRCC1_N	1	62	3.5e-14	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000142629

Predicted Effect

probably benign
Transcript: ENSMUST00000146450

SMART Domains

Protein: ENSMUSP00000117300
Gene: ENSMUSG00000099481

Domain	Start	End	E-Value	Type
Pfam:XRCC1_N	1	152	1.1e-29	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000155078

SMART Domains

Protein: ENSMUSP00000123466
Gene: ENSMUSG00000070425

Domain	Start	End	E-Value	Type
Pfam:XRCC1_N	1	62	4.4e-22	PFAM

Meta Mutation Damage Score

0.0846

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.6%
20x: 98.7%

Validation Efficiency

98% (55/56)

Allele List at MGI

Other mutations in this stock

Total: 55 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Accs	A	C	2: 93,668,403 (GRCm39)	L356R	probably damaging	Het
Acvr1	A	T	2: 58,338,422 (GRCm39)	D433E	possibly damaging	Het
Aldh3b1	A	G	19: 3,971,502 (GRCm39)	L122P	probably damaging	Het
Ap3b1	T	G	13: 94,540,586 (GRCm39)	N169K	possibly damaging	Het
Apbb2	A	G	5: 66,609,000 (GRCm39)	S216P	probably benign	Het
Arap3	T	A	18: 38,130,077 (GRCm39)	H28L	possibly damaging	Het
Arhgap44	C	T	11: 64,898,896 (GRCm39)	M760I	possibly damaging	Het
Arhgef19	G	T	4: 140,975,193 (GRCm39)	A304S	probably benign	Het
Atpaf1	T	C	4: 115,645,548 (GRCm39)	I139T	possibly damaging	Het
BC024139	G	T	15: 76,010,320 (GRCm39)	T62K	possibly damaging	Het
Bmal2	G	A	6: 146,723,492 (GRCm39)	G274D	probably benign	Het
Capn5	T	C	7: 97,780,902 (GRCm39)	T292A	probably benign	Het
Card19	T	C	13: 49,358,814 (GRCm39)	N53S	possibly damaging	Het
Cep97	A	G	16: 55,742,467 (GRCm39)	V232A	possibly damaging	Het
Cfap298	A	G	16: 90,724,281 (GRCm39)	I164T	possibly damaging	Het
Clca3a2	G	T	3: 144,777,360 (GRCm39)	T837K	probably benign	Het
Col8a2	G	C	4: 126,204,647 (GRCm39)	G219A	probably damaging	Het
Ctu2	T	C	8: 123,206,951 (GRCm39)	S365P		Het
Dnah2	T	C	11: 69,382,348 (GRCm39)	D1254G	probably damaging	Het
Dscam	A	G	16: 96,420,828 (GRCm39)	L1686S	probably damaging	Het
Fgr	A	G	4: 132,726,071 (GRCm39)		probably benign	Het
Frmd4a	T	A	2: 4,606,111 (GRCm39)	S612T	probably damaging	Het
Gadd45gip1	T	C	8: 85,560,748 (GRCm39)	I121T	probably damaging	Het
Gapvd1	A	G	2: 34,568,560 (GRCm39)	V1353A	possibly damaging	Het
Gdf3	G	A	6: 122,583,942 (GRCm39)	P142S	probably damaging	Het
Gm19965	G	A	1: 116,749,776 (GRCm39)	G486R	unknown	Het
Gpatch2l	T	C	12: 86,308,405 (GRCm39)	L307P	probably damaging	Het
Grm3	T	C	5: 9,561,580 (GRCm39)	K757E	probably damaging	Het
Inppl1	T	A	7: 101,472,750 (GRCm39)	H1218L	possibly damaging	Het
Jag2	T	C	12: 112,873,257 (GRCm39)	I1055V	probably benign	Het
Krtap9-5	G	T	11: 99,840,340 (GRCm39)	C347F	unknown	Het
Magi2	T	A	5: 20,856,190 (GRCm39)	Y1050*	probably null	Het
Myrf	A	G	19: 10,206,378 (GRCm39)		probably benign	Het
Ntpcr	T	G	8: 126,464,785 (GRCm39)		probably benign	Het
Or13a19	T	C	7: 139,902,716 (GRCm39)	Y35H	probably damaging	Het
Or1p1b	C	T	11: 74,130,846 (GRCm39)	T152I	probably damaging	Het
Or2y1c	T	C	11: 49,361,386 (GRCm39)	M136T	probably damaging	Het
Palmd	T	G	3: 116,720,899 (GRCm39)	D145A	probably damaging	Het
Pdcd1	A	G	1: 93,980,155 (GRCm39)	S21P	probably benign	Het
Pkn1	T	C	8: 84,398,879 (GRCm39)	T696A	possibly damaging	Het
Pnpt1	T	A	11: 29,096,769 (GRCm39)		probably benign	Het
Sbf2	T	A	7: 110,049,146 (GRCm39)	I273F	probably damaging	Het
Skic3	T	G	13: 76,323,403 (GRCm39)	D1382E	probably benign	Het
Slc16a4	A	T	3: 107,208,101 (GRCm39)	N204Y	probably benign	Het
Slc38a1	T	C	15: 96,514,091 (GRCm39)	I44V	possibly damaging	Het
Smpdl3a	T	C	10: 57,685,166 (GRCm39)	V312A	probably damaging	Het
Ston1	A	G	17: 88,942,600 (GRCm39)	Y2C	probably benign	Het
Syde1	A	T	10: 78,425,325 (GRCm39)	Y229N	probably damaging	Het
Ttc6	T	A	12: 57,784,489 (GRCm39)	C1853S	possibly damaging	Het
Ttn	A	G	2: 76,609,249 (GRCm39)	I17650T	possibly damaging	Het
Upf1	T	C	8: 70,796,918 (GRCm39)	E105G	possibly damaging	Het
Wrn	A	G	8: 33,814,422 (GRCm39)	W341R	probably benign	Het
Zbtb26	T	C	2: 37,326,896 (GRCm39)	T47A	probably benign	Het
Zc3h10	A	T	10: 128,380,163 (GRCm39)	V398E	probably damaging	Het
Zfp652	G	T	11: 95,639,921 (GRCm39)		probably benign	Het

Other mutations in Xndc1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
R0415:Xndc1	UTSW	7	101,729,823 (GRCm39)	splice site	probably benign
R0648:Xndc1	UTSW	7	101,728,031 (GRCm39)	missense	possibly damaging	0.46
R1990:Xndc1	UTSW	7	101,722,398 (GRCm39)	missense	probably damaging	1.00
R1991:Xndc1	UTSW	7	101,722,398 (GRCm39)	missense	probably damaging	1.00
R4290:Xndc1	UTSW	7	101,730,694 (GRCm39)	missense	possibly damaging	0.95
R4295:Xndc1	UTSW	7	101,730,694 (GRCm39)	missense	possibly damaging	0.95
R4530:Xndc1	UTSW	7	101,727,942 (GRCm39)	missense	probably benign	0.21
R4815:Xndc1	UTSW	7	101,722,523 (GRCm39)	missense	probably null	1.00
R5384:Xndc1	UTSW	7	101,731,395 (GRCm39)	missense	probably benign	0.12
R6838:Xndc1	UTSW	7	101,722,476 (GRCm39)	missense	possibly damaging	0.79
R6940:Xndc1	UTSW	7	101,727,094 (GRCm39)	missense	probably benign	0.15
R7310:Xndc1	UTSW	7	101,727,938 (GRCm39)	critical splice acceptor site	probably null
R7375:Xndc1	UTSW	7	101,730,687 (GRCm39)	splice site	probably null
R8271:Xndc1	UTSW	7	101,728,343 (GRCm39)	missense	possibly damaging	0.58
R8802:Xndc1	UTSW	7	101,720,539 (GRCm39)	missense	possibly damaging	0.84
R8996:Xndc1	UTSW	7	101,722,518 (GRCm39)	missense	probably damaging	1.00
R9230:Xndc1	UTSW	7	101,722,476 (GRCm39)	missense	probably damaging	1.00
R9716:Xndc1	UTSW	7	101,725,114 (GRCm39)	missense	probably damaging	1.00
X0060:Xndc1	UTSW	7	101,728,355 (GRCm39)	missense	probably benign	0.08
X0065:Xndc1	UTSW	7	101,730,692 (GRCm39)	missense	probably benign	0.03

Predicted Primers

PCR Primer
(F):5'- AGGCCTTCAGGAAATAGCTAGAC -3'
(R):5'- TCTGTCCCCATAGACACCAG -3'

Sequencing Primer
(F):5'- CCTTCAGGAAATAGCTAGACTGTTTG -3'
(R):5'- GTCCAGCAGTCCTAGTTGTCAAATG -3'

Posted On

2021-07-15