Mutagenetix > Incidental Mutation

Incidental Mutation 'R5308:Xpa'

434465

Institutional Source

Beutler Lab

Gene Symbol

Xpa

Ensembl Gene

ENSMUSG00000028329

Gene Name

xeroderma pigmentosum, complementation group A

Synonyms

Xpac

MMRRC Submission

042891-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R5308 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

46175222-46196345 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 46185659 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Glutamic Acid to Aspartic acid at position 106 (E106D)

Ref Sequence

ENSEMBL: ENSMUSP00000050453 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000030013] [ENSMUST00000058232] [ENSMUST00000132358] [ENSMUST00000142380]

AlphaFold

Q64267

Predicted Effect

probably benign
Transcript: ENSMUST00000030013
AA Change: E106D

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)

SMART Domains

Protein: ENSMUSP00000030013
Gene: ENSMUSG00000028329
AA Change: E106D

Domain	Start	End	E-Value	Type
low complexity region	32	55	N/A	INTRINSIC
Pfam:XPA_N	99	132	1.5e-20	PFAM
Pfam:XPA_C	133	185	3.7e-28	PFAM
low complexity region	212	223	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000058232
AA Change: E106D

PolyPhen 2 Score 0.002 (Sensitivity: 0.99; Specificity: 0.30)

SMART Domains

Protein: ENSMUSP00000050453
Gene: ENSMUSG00000028329
AA Change: E106D

Domain	Start	End	E-Value	Type
low complexity region	32	55	N/A	INTRINSIC
Pfam:XPA_N	101	132	5.2e-18	PFAM
Pfam:XPA_C	134	185	3e-30	PFAM
low complexity region	212	223	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000130051

Predicted Effect

probably benign
Transcript: ENSMUST00000132358

SMART Domains

Protein: ENSMUSP00000138512
Gene: ENSMUSG00000028329

Domain	Start	End	E-Value	Type
Pfam:XPA_N	1	23	1.1e-13	PFAM
Pfam:XPA_C	24	76	7.9e-29	PFAM
low complexity region	103	114	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000141318

Predicted Effect

probably benign
Transcript: ENSMUST00000142380
AA Change: E106D

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)

SMART Domains

Protein: ENSMUSP00000121850
Gene: ENSMUSG00000028329
AA Change: E106D

Domain	Start	End	E-Value	Type
low complexity region	32	55	N/A	INTRINSIC
Pfam:XPA_N	99	132	1.5e-20	PFAM
Pfam:XPA_C	133	185	3.7e-28	PFAM
low complexity region	212	225	N/A	INTRINSIC

Coding Region Coverage

1x: 99.2%
3x: 97.7%
10x: 95.4%
20x: 91.2%

Validation Efficiency

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a zinc finger protein involved in DNA excision repair. The encoded protein is part of the NER (nucleotide excision repair) complext which is responsible for repair of UV radiation-induced photoproducts and DNA adducts induced by chemical carcinogens. Mutations in this gene are associated with xeroderma pigmentosum complementation group A. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Mar 2009]
PHENOTYPE: Homozygous null mutants are highly susceptible to tumors induced by UV (skin and ocular tumors), 7,12-dimethylbenz[a]anthracene (skin tumors), benzo[a]pyrene (pulmonary tumors), 4-nitroquinoline-1-oxide (tongue tumors) and aflatoxin B(1) (liver tumors). [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 65 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1700006A11Rik	C	G	3: 124,199,999 (GRCm39)	G531A	probably damaging	Het
4921504E06Rik	T	C	2: 19,528,892 (GRCm39)	D163G	probably damaging	Het
Abcd4	C	T	12: 84,650,067 (GRCm39)		probably null	Het
Alg9	T	C	9: 50,734,011 (GRCm39)	S570P	possibly damaging	Het
Angptl3	C	A	4: 98,922,723 (GRCm39)	H255N	probably benign	Het
Ank3	G	A	10: 69,838,395 (GRCm39)	R1566K	possibly damaging	Het
Cdc37	A	T	9: 21,052,060 (GRCm39)	D326E	probably benign	Het
Cdk13	T	C	13: 17,946,898 (GRCm39)	K6R	probably damaging	Het
Ces1b	T	C	8: 93,793,645 (GRCm39)	K315E	probably benign	Het
Cfap61	G	A	2: 145,951,908 (GRCm39)	G190S	probably damaging	Het
Cimap3	T	C	3: 105,908,419 (GRCm39)	T107A	probably benign	Het
Ckap4	T	C	10: 84,364,238 (GRCm39)	E275G	probably benign	Het
Cplane1	G	A	15: 8,290,174 (GRCm39)		probably null	Het
Csf3r	A	G	4: 125,929,137 (GRCm39)	D349G	probably benign	Het
Cyp2d37-ps	T	C	15: 82,574,012 (GRCm39)		noncoding transcript	Het
Dmbt1	T	A	7: 130,642,751 (GRCm39)	C190S	probably damaging	Het
Dnah11	A	G	12: 118,049,415 (GRCm39)	F1670L	possibly damaging	Het
Dnah5	A	T	15: 28,229,797 (GRCm39)	I144F	possibly damaging	Het
Eno2	C	A	6: 124,744,056 (GRCm39)	V84L	probably damaging	Het
Ercc4	G	T	16: 12,948,028 (GRCm39)	R325L	probably damaging	Het
Fcgr2b	T	G	1: 170,793,279 (GRCm39)	Q250P	probably benign	Het
Garin5a	T	C	7: 44,149,606 (GRCm39)	V109A	probably damaging	Het
Garre1	T	A	7: 33,945,180 (GRCm39)	K355*	probably null	Het
Gcfc2	T	C	6: 81,920,524 (GRCm39)		probably null	Het
Glb1l2	C	T	9: 26,676,055 (GRCm39)	G509D	probably damaging	Het
Gm11595	G	A	11: 99,663,381 (GRCm39)	R100C	unknown	Het
Grn	A	G	11: 102,327,018 (GRCm39)	N160D	possibly damaging	Het
Hexd	T	A	11: 121,113,095 (GRCm39)	V510D	probably damaging	Het
Igfbp1	G	A	11: 7,149,919 (GRCm39)		probably null	Het
Itga11	T	A	9: 62,663,051 (GRCm39)	M589K	probably benign	Het
Itpr1	A	T	6: 108,333,472 (GRCm39)	S51C	probably damaging	Het
Klra3	T	C	6: 130,311,270 (GRCm39)		probably null	Het
Mad2l1	T	C	6: 66,514,675 (GRCm39)		probably null	Het
Matn3	CGGGGCTCGGGGGC	CGGGGC	12: 9,002,308 (GRCm39)		probably null	Het
Myo9a	T	A	9: 59,771,244 (GRCm39)	Y939N	probably damaging	Het
Nxpe3	C	T	16: 55,686,834 (GRCm39)	S58N	probably benign	Het
Or1j16	T	A	2: 36,530,706 (GRCm39)	Y218*	probably null	Het
Or3a1c	T	A	11: 74,046,397 (GRCm39)	M139K	probably damaging	Het
Or4c103	T	C	2: 88,513,749 (GRCm39)	E109G	probably benign	Het
Or4k45	C	T	2: 111,394,899 (GRCm39)	A297T	probably damaging	Het
Paics	T	C	5: 77,104,479 (GRCm39)	S35P	probably damaging	Het
Pcnt	A	C	10: 76,192,159 (GRCm39)	Y2717*	probably null	Het
Plekho2	T	A	9: 65,465,957 (GRCm39)	N144Y	probably damaging	Het
Plscr5	T	C	9: 92,080,565 (GRCm39)	F17S	possibly damaging	Het
Prrc2a	C	T	17: 35,380,023 (GRCm39)	R192H	unknown	Het
Rbm27	T	A	18: 42,460,275 (GRCm39)	M735K	probably damaging	Het
Rfc1	T	A	5: 65,436,804 (GRCm39)	K625N	probably damaging	Het
Ric8b	T	A	10: 84,783,611 (GRCm39)	F156L	probably benign	Het
Romo1	C	A	2: 155,986,473 (GRCm39)	A32E	possibly damaging	Het
Rpl26	T	A	11: 68,795,284 (GRCm39)	Y135N	probably damaging	Het
Sacs	T	C	14: 61,429,849 (GRCm39)	V636A	probably benign	Het
Scyl2	A	T	10: 89,477,869 (GRCm39)	I710N	probably benign	Het
Sh3bp5	C	A	14: 31,099,452 (GRCm39)	R265L	probably benign	Het
Slc4a1	T	A	11: 102,249,903 (GRCm39)	I154F	probably damaging	Het
Snx11	A	G	11: 96,661,535 (GRCm39)	S157P	probably damaging	Het
Snx18	G	A	13: 113,753,383 (GRCm39)	Q517*	probably null	Het
Stard4	G	T	18: 33,336,678 (GRCm39)	N212K	probably damaging	Het
Strn3	A	G	12: 51,676,168 (GRCm39)	Y454H	probably damaging	Het
Stx17	A	T	4: 48,182,851 (GRCm39)		probably benign	Het
Tas2r121	G	A	6: 132,677,480 (GRCm39)	T164I	possibly damaging	Het
Tbc1d8	T	C	1: 39,428,490 (GRCm39)	Y485C	probably damaging	Het
Tmem45b	T	C	9: 31,340,380 (GRCm39)	M8V	probably damaging	Het
Usp28	T	C	9: 48,948,501 (GRCm39)	F844L	probably damaging	Het
Usp32	T	A	11: 84,908,544 (GRCm39)	N1054I	probably benign	Het
Zfp85	C	T	13: 67,896,974 (GRCm39)	C366Y	probably damaging	Het

Other mutations in Xpa

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL02127:Xpa	APN	4	46,185,606 (GRCm39)	missense	probably damaging	1.00
IGL02670:Xpa	APN	4	46,185,682 (GRCm39)	missense	probably benign	0.03
R1863:Xpa	UTSW	4	46,155,730 (GRCm39)	intron	probably benign
R2149:Xpa	UTSW	4	46,183,189 (GRCm39)	missense	probably damaging	0.99
R4534:Xpa	UTSW	4	46,185,624 (GRCm39)	missense	probably benign	0.00
R6647:Xpa	UTSW	4	46,183,089 (GRCm39)	missense	probably benign	0.00
R7157:Xpa	UTSW	4	46,185,612 (GRCm39)	missense	probably damaging	1.00
R7185:Xpa	UTSW	4	46,183,078 (GRCm39)	missense	probably benign
R8191:Xpa	UTSW	4	46,183,225 (GRCm39)	missense	possibly damaging	0.56
R8219:Xpa	UTSW	4	46,183,150 (GRCm39)	missense	probably benign	0.02
Z1177:Xpa	UTSW	4	46,183,036 (GRCm39)	missense	probably benign	0.09

Predicted Primers

PCR Primer
(F):5'- TCCCTAGAGAGAAGAGCCAG -3'
(R):5'- AACCTAAGGTTAATCAGTTTCTCCC -3'

Sequencing Primer
(F):5'- GACCCAGAAATCTCCACTTGGG -3'
(R):5'- CCCCAGTAAGCATTTGTGTCAGG -3'

Posted On

2016-10-06