Mutagenetix > Incidental Mutation

Incidental Mutation 'R3855:Apex1'

276133

Institutional Source

Beutler Lab

Gene Symbol

Apex1

Ensembl Gene

ENSMUSG00000035960

Gene Name

apurinic/apyrimidinic endonuclease 1

Synonyms

Ref-1, HAP1

MMRRC Submission

040901-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R3855 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

51162425-51164596 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 51163714 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Threonine to Alanine at position 109 (T109A)

Ref Sequence

ENSEMBL: ENSMUSP00000116319 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000006452] [ENSMUST00000049312] [ENSMUST00000049411] [ENSMUST00000128395] [ENSMUST00000136753] [ENSMUST00000154288] [ENSMUST00000160393] [ENSMUST00000160538] [ENSMUST00000160835] [ENSMUST00000160375] [ENSMUST00000162177] [ENSMUST00000159292] [ENSMUST00000162957] [ENSMUST00000160890] [ENSMUST00000161166] [ENSMUST00000226871]

AlphaFold

P28352

Predicted Effect

probably benign
Transcript: ENSMUST00000006452

SMART Domains

Protein: ENSMUSP00000006452
Gene: ENSMUSG00000006289

Domain	Start	End	E-Value	Type
Pfam:Peptidase_M22	23	186	1.1e-55	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000049312

SMART Domains

Protein: ENSMUSP00000038276
Gene: ENSMUSG00000035953

Domain	Start	End	E-Value	Type
Pfam:Tmemb_55A	1	270	9.8e-132	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000049411
AA Change: T114A

PolyPhen 2 Score 0.066 (Sensitivity: 0.94; Specificity: 0.84)

SMART Domains

Protein: ENSMUSP00000042602
Gene: ENSMUSG00000035960
AA Change: T114A

Domain	Start	End	E-Value	Type
low complexity region	14	40	N/A	INTRINSIC
Pfam:Exo_endo_phos	64	308	1.5e-31	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000128395
AA Change: T109A

PolyPhen 2 Score 0.128 (Sensitivity: 0.93; Specificity: 0.86)

SMART Domains

Protein: ENSMUSP00000116319
Gene: ENSMUSG00000035960
AA Change: T109A

Domain	Start	End	E-Value	Type
low complexity region	9	35	N/A	INTRINSIC
Pfam:Exo_endo_phos	59	280	2.3e-24	PFAM
Pfam:Exo_endo_phos_2	138	284	4e-12	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000136753
AA Change: T114A

PolyPhen 2 Score 0.066 (Sensitivity: 0.94; Specificity: 0.84)

SMART Domains

Protein: ENSMUSP00000123148
Gene: ENSMUSG00000035960
AA Change: T114A

Domain	Start	End	E-Value	Type
low complexity region	14	40	N/A	INTRINSIC
Pfam:Exo_endo_phos	64	177	3.8e-13	PFAM

Predicted Effect

unknown
Transcript: ENSMUST00000154288
AA Change: T114A

SMART Domains

Protein: ENSMUSP00000122343
Gene: ENSMUSG00000035960
AA Change: T114A

Domain	Start	End	E-Value	Type
low complexity region	14	40	N/A	INTRINSIC
Pfam:Exo_endo_phos	64	214	1.1e-18	PFAM

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000159047

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000162935

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000160464

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000159745

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000163043

Predicted Effect

probably benign
Transcript: ENSMUST00000160393

SMART Domains

Protein: ENSMUSP00000125155
Gene: ENSMUSG00000006289

Domain	Start	End	E-Value	Type
Pfam:Peptidase_M22	23	301	3.6e-90	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000160538

SMART Domains

Protein: ENSMUSP00000124259
Gene: ENSMUSG00000035953

Domain	Start	End	E-Value	Type
Pfam:Tmemb_55A	1	197	1.9e-82	PFAM
low complexity region	221	235	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000160835

SMART Domains

Protein: ENSMUSP00000124782
Gene: ENSMUSG00000035953

Domain	Start	End	E-Value	Type
Pfam:Tmemb_55A	4	277	2.8e-129	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000160375

SMART Domains

Protein: ENSMUSP00000124099
Gene: ENSMUSG00000006289

Domain	Start	End	E-Value	Type
Pfam:Peptidase_M22	1	156	1.3e-45	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000162177

SMART Domains

Protein: ENSMUSP00000124016
Gene: ENSMUSG00000006289

Domain	Start	End	E-Value	Type
Pfam:Peptidase_M22	1	220	1.1e-68	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000159292

SMART Domains

Protein: ENSMUSP00000124039
Gene: ENSMUSG00000006289

Domain	Start	End	E-Value	Type
Pfam:Peptidase_M22	23	301	3.6e-90	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000162957

SMART Domains

Protein: ENSMUSP00000123697
Gene: ENSMUSG00000035953

Domain	Start	End	E-Value	Type
Pfam:Tmemb_55A	1	174	2.9e-64	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000160890

SMART Domains

Protein: ENSMUSP00000124659
Gene: ENSMUSG00000006289

Domain	Start	End	E-Value	Type
Pfam:Peptidase_M22	23	79	1.7e-14	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000161669

Predicted Effect

probably benign
Transcript: ENSMUST00000161166

SMART Domains

Protein: ENSMUSP00000125414
Gene: ENSMUSG00000035953

Domain	Start	End	E-Value	Type
Pfam:Tmemb_55A	1	168	3.6e-65	PFAM

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000163088

Predicted Effect

probably benign
Transcript: ENSMUST00000226871

Meta Mutation Damage Score

0.0898

Coding Region Coverage

1x: 99.6%
3x: 98.7%
10x: 96.9%
20x: 93.3%

Validation Efficiency

98% (45/46)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] Apurinic/apyrimidinic (AP) sites occur frequently in DNA molecules by spontaneous hydrolysis, by DNA damaging agents or by DNA glycosylases that remove specific abnormal bases. AP sites are pre-mutagenic lesions that can prevent normal DNA replication so the cell contains systems to identify and repair such sites. Class II AP endonucleases cleave the phosphodiester backbone 5' to the AP site. This gene encodes the major AP endonuclease in human cells. Splice variants have been found for this gene; all encode the same protein. [provided by RefSeq, Jul 2008]
PHENOTYPE: Mice homozygous for a knock-out allele exhibit embryonic lethality prior to E10 associated with abnormal embryogenesis. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 45 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Akna	A	T	4: 63,291,705 (GRCm39)	S1144R	probably damaging	Het
Apbb1ip	T	C	2: 22,765,187 (GRCm39)	S623P	unknown	Het
Arhgef1	G	A	7: 24,618,697 (GRCm39)	G107S	probably damaging	Het
Ccnq	T	C	11: 78,642,013 (GRCm39)	N159S	probably benign	Het
Cdc42bpa	A	G	1: 179,983,543 (GRCm39)		probably benign	Het
Cog2	T	C	8: 125,256,742 (GRCm39)		probably null	Het
Dennd4c	G	A	4: 86,698,084 (GRCm39)	V191M	probably damaging	Het
Dthd1	T	A	5: 62,984,472 (GRCm39)	H392Q	probably benign	Het
Dthd1	T	C	5: 63,045,366 (GRCm39)	V710A	probably benign	Het
Galnt7	T	C	8: 57,985,658 (GRCm39)		probably benign	Het
Gm4868	A	G	5: 125,925,609 (GRCm39)		noncoding transcript	Het
Gpr179	T	C	11: 97,232,260 (GRCm39)	E648G	probably damaging	Het
Hk2	T	C	6: 82,713,657 (GRCm39)	E447G	possibly damaging	Het
Idi1	G	T	13: 8,935,968 (GRCm39)	A25S	probably benign	Het
Itgb3bp	T	C	4: 99,686,957 (GRCm39)	E76G	possibly damaging	Het
Khk	A	G	5: 31,084,401 (GRCm39)	D82G	probably benign	Het
Kif17	A	G	4: 138,018,821 (GRCm39)	S533G	probably benign	Het
Kmt2a	A	G	9: 44,741,796 (GRCm39)		probably benign	Het
Kmt5c	T	C	7: 4,749,255 (GRCm39)	F104S	probably damaging	Het
Lmf1	G	A	17: 25,873,445 (GRCm39)	V317M	probably damaging	Het
Mdh1	C	T	11: 21,509,281 (GRCm39)	V234I	probably benign	Het
Nbas	T	A	12: 13,329,415 (GRCm39)	I120N	possibly damaging	Het
Nfia	A	G	4: 97,951,259 (GRCm39)	H362R	probably damaging	Het
Nhlrc2	T	C	19: 56,576,703 (GRCm39)		probably null	Het
Nme5	A	G	18: 34,702,884 (GRCm39)	S135P	possibly damaging	Het
Nt5c2	A	G	19: 46,884,957 (GRCm39)	V252A	probably damaging	Het
Nufip2	T	C	11: 77,583,715 (GRCm39)	V543A	probably damaging	Het
Or1l4b	A	T	2: 37,036,835 (GRCm39)	I204F	possibly damaging	Het
Or2y10	A	G	11: 49,454,918 (GRCm39)	T57A	probably damaging	Het
Otog	T	C	7: 45,923,184 (GRCm39)	S1020P	possibly damaging	Het
Pear1	T	C	3: 87,659,228 (GRCm39)	H814R	possibly damaging	Het
Pkd1l1	A	G	11: 8,915,047 (GRCm39)		probably null	Het
Pla2g4a	T	A	1: 149,705,928 (GRCm39)	I711F	possibly damaging	Het
Ppig	G	A	2: 69,579,719 (GRCm39)	V418I	unknown	Het
Prg4	T	C	1: 150,327,751 (GRCm39)	Y234C	probably damaging	Het
Prmt9	G	A	8: 78,294,894 (GRCm39)	V413I	probably benign	Het
Rnf145	G	A	11: 44,422,120 (GRCm39)	V68M	possibly damaging	Het
Sepsecs	G	A	5: 52,821,616 (GRCm39)	R74C	probably damaging	Het
Sgsm1	A	G	5: 113,411,125 (GRCm39)	V580A	probably benign	Het
Sh3bp1	C	T	15: 78,785,361 (GRCm39)		probably benign	Het
Sox11	C	A	12: 27,391,501 (GRCm39)	G303C	probably damaging	Het
Usp54	C	A	14: 20,638,488 (GRCm39)	M197I	probably damaging	Het
Vps26c	A	G	16: 94,311,665 (GRCm39)	F95L	probably benign	Het
Xylt1	T	G	7: 117,192,777 (GRCm39)	L361R	probably damaging	Het
Zfp512	A	G	5: 31,637,593 (GRCm39)	R505G	possibly damaging	Het

Other mutations in Apex1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01025:Apex1	APN	14	51,163,711 (GRCm39)	missense	possibly damaging	0.47
R3856:Apex1	UTSW	14	51,163,714 (GRCm39)	missense	probably benign	0.13
R4461:Apex1	UTSW	14	51,163,970 (GRCm39)	missense	probably damaging	0.99
R6014:Apex1	UTSW	14	51,162,982 (GRCm39)	missense	probably benign	0.00
R6212:Apex1	UTSW	14	51,164,350 (GRCm39)	missense	probably benign	0.18
R7653:Apex1	UTSW	14	51,163,995 (GRCm39)	missense	probably damaging	1.00
R9206:Apex1	UTSW	14	51,163,125 (GRCm39)	missense	possibly damaging	0.81

Predicted Primers

PCR Primer
(F):5'- ATTCTGCTGCTCGAATGCC -3'
(R):5'- ACAATCACCCGGCCTTCTTG -3'

Sequencing Primer
(F):5'- AATGCCTTCTGTGTATAGCATGTAGC -3'
(R):5'- ACCCGGCCTTCTTGATCATG -3'

Posted On

2015-04-06