Mutagenetix > Incidental Mutation

Incidental Mutation 'R8219:Xpa'

636532

Institutional Source

Beutler Lab

Gene Symbol

Xpa

Ensembl Gene

ENSMUSG00000028329

Gene Name

xeroderma pigmentosum, complementation group A

Synonyms

Xpac

MMRRC Submission

067659-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R8219 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

46175222-46196345 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to T at 46183150 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Methionine to Lysine at position 213 (M213K)

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: M213K

PolyPhen 2 Score 0.015 (Sensitivity: 0.96; Specificity: 0.79)

SMART Domains

Protein: ENSMUSP00000030013
Gene: ENSMUSG00000028329
AA Change: M213K

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: M213K

PolyPhen 2 Score 0.024 (Sensitivity: 0.95; Specificity: 0.81)

SMART Domains

Protein: ENSMUSP00000050453
Gene: ENSMUSG00000028329
AA Change: M213K

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

probably benign
Transcript: ENSMUST00000132358
AA Change: M104K

PolyPhen 2 Score 0.019 (Sensitivity: 0.95; Specificity: 0.80)

SMART Domains

Protein: ENSMUSP00000138512
Gene: ENSMUSG00000028329
AA Change: M104K

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

probably benign
Transcript: ENSMUST00000142380
AA Change: M213K

PolyPhen 2 Score 0.041 (Sensitivity: 0.94; Specificity: 0.83)

SMART Domains

Protein: ENSMUSP00000121850
Gene: ENSMUSG00000028329
AA Change: M213K

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: 99.9%
3x: 99.8%
10x: 99.5%
20x: 98.7%

Validation Efficiency

100% (62/62)

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
4933414I15Rik	A	T	11: 50,833,363 (GRCm39)	S80T	unknown	Het
Acnat1	T	A	4: 49,447,748 (GRCm39)	I278F	probably benign	Het
Adgrf5	A	T	17: 43,760,750 (GRCm39)	Q815L	probably benign	Het
Aff1	T	A	5: 103,994,199 (GRCm39)	Y1022N	probably damaging	Het
Ahi1	A	G	10: 20,950,335 (GRCm39)	K1034E	probably benign	Het
Ano8	A	T	8: 71,933,357 (GRCm39)	L645Q	unknown	Het
Atg9b	A	G	5: 24,591,330 (GRCm39)	L756P	probably damaging	Het
Atp2b2	A	T	6: 113,770,811 (GRCm39)	I411N	probably damaging	Het
Bmp6	T	A	13: 38,529,963 (GRCm39)	C19S	unknown	Het
Borcs5	A	G	6: 134,621,313 (GRCm39)	H27R	probably benign	Het
Cachd1	C	A	4: 100,848,159 (GRCm39)	D1091E	probably benign	Het
Ccdc186	T	A	19: 56,781,777 (GRCm39)	M801L	probably benign	Het
Clcn3	A	T	8: 61,376,000 (GRCm39)	M658K	probably damaging	Het
Col1a1	C	T	11: 94,834,184 (GRCm39)	R500C	probably damaging	Het
Cul4a	T	A	8: 13,196,540 (GRCm39)	D731E	possibly damaging	Het
Dnajb8	C	T	6: 88,199,940 (GRCm39)	R159C	possibly damaging	Het
E2f7	T	A	10: 110,595,704 (GRCm39)	V133E	probably damaging	Het
Fam161b	T	C	12: 84,393,648 (GRCm39)	E575G	probably benign	Het
Fubp1	T	A	3: 151,926,103 (GRCm39)	V275D	probably damaging	Het
Gabrg1	T	A	5: 70,931,643 (GRCm39)	R367*	probably null	Het
Gm6902	G	A	7: 22,973,143 (GRCm39)	A128V	probably benign	Het
Gnptab	A	G	10: 88,269,654 (GRCm39)	T786A	probably benign	Het
Golga2	A	G	2: 32,196,492 (GRCm39)	N981D	probably damaging	Het
Gsap	A	T	5: 21,456,113 (GRCm39)	I437L	probably benign	Het
Gulp1	A	G	1: 44,793,501 (GRCm39)		probably null	Het
Kcnn1	T	C	8: 71,305,499 (GRCm39)	Y237C	probably damaging	Het
Klhl28	A	T	12: 64,998,431 (GRCm39)	N354K	probably benign	Het
Lama3	T	C	18: 12,572,417 (GRCm39)	Y541H	probably benign	Het
Lamc1	A	G	1: 153,123,073 (GRCm39)	Y706H	probably damaging	Het
Lima1	G	T	15: 99,678,671 (GRCm39)	T590K	probably damaging	Het
Lrrc38	G	A	4: 143,077,303 (GRCm39)	G189R	probably damaging	Het
Mrgprb8	G	A	7: 48,038,649 (GRCm39)	V107M	possibly damaging	Het
Mrpl3	T	A	9: 104,934,271 (GRCm39)	N139K	possibly damaging	Het
Nhsl3	T	A	4: 129,141,946 (GRCm39)	D65V	possibly damaging	Het
Nudt16	T	A	9: 105,007,636 (GRCm39)	N161I	probably damaging	Het
Obscn	G	A	11: 59,013,574 (GRCm39)	S1091L	probably benign	Het
Oog4	T	C	4: 143,166,508 (GRCm39)	M99V	probably benign	Het
Or5b105	A	C	19: 13,080,284 (GRCm39)	L122R	probably damaging	Het
Or8c16	A	C	9: 38,130,668 (GRCm39)	D183A	probably damaging	Het
Osbpl6	A	T	2: 76,386,247 (GRCm39)	D303V	probably damaging	Het
Pcdhb21	T	C	18: 37,647,708 (GRCm39)	F279S	probably damaging	Het
Peg3	G	A	7: 6,711,364 (GRCm39)	T1286I	probably benign	Het
Phax	A	G	18: 56,708,754 (GRCm39)	N106S	probably damaging	Het
Pkdrej	A	G	15: 85,705,493 (GRCm39)	Y148H	probably damaging	Het
Pramel20	T	G	4: 143,298,530 (GRCm39)	Y158D	probably benign	Het
Ptprn2	C	A	12: 117,148,357 (GRCm39)	Q706K	probably benign	Het
Rdh11	T	G	12: 79,235,880 (GRCm39)	K23Q	probably benign	Het
Rit2	T	A	18: 31,108,547 (GRCm39)	E146V	probably damaging	Het
Rnf141	T	C	7: 110,436,472 (GRCm39)		probably benign	Het
Sars1	T	A	3: 108,352,378 (GRCm39)	E24V	probably benign	Het
Sh3tc2	A	G	18: 62,144,932 (GRCm39)	I1129V	probably benign	Het
Slc10a5	G	T	3: 10,400,384 (GRCm39)	P92Q	probably benign	Het
Slc24a5	A	T	2: 124,927,575 (GRCm39)		probably null	Het
Slc5a8	A	G	10: 88,757,561 (GRCm39)	Y517C	probably damaging	Het
Slc6a5	A	G	7: 49,561,911 (GRCm39)	M148V	probably benign	Het
Sorl1	T	C	9: 41,952,857 (GRCm39)		probably null	Het
Tgm4	A	T	9: 122,874,117 (GRCm39)	Y119F	probably benign	Het
Tgm6	A	G	2: 129,993,200 (GRCm39)	K562R	probably benign	Het
Tlr3	T	C	8: 45,851,016 (GRCm39)	E627G	possibly damaging	Het
Tmprss11f	A	G	5: 86,677,878 (GRCm39)	L297P	probably damaging	Het
Tpbgl	T	C	7: 99,274,978 (GRCm39)	H293R	probably benign	Het
Trank1	A	C	9: 111,193,977 (GRCm39)	K667T	probably damaging	Het
Trpm1	A	T	7: 63,851,699 (GRCm39)	Q139L	probably benign	Het
Ttf2	T	G	3: 100,869,879 (GRCm39)	K398T	possibly damaging	Het
Zmym2	T	A	14: 57,163,316 (GRCm39)	S623T	probably benign	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
R5308:Xpa	UTSW	4	46,185,659 (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
Z1177:Xpa	UTSW	4	46,183,036 (GRCm39)	missense	probably benign	0.09

Predicted Primers

PCR Primer
(F):5'- GATGCCTAATCCCACTGTCC -3'
(R):5'- ATGACATCTGTGAGCTCGAC -3'

Sequencing Primer
(F):5'- TGACTTACATGAAAACGATGGCC -3'
(R):5'- CATCTGTGAGCTCGACAGTTAGGAC -3'

Posted On

2020-07-13