Mutagenetix > Incidental Mutation

Incidental Mutation 'R9712:Pms2'

730247

Institutional Source

Beutler Lab

Gene Symbol

Pms2

Ensembl Gene

ENSMUSG00000079109

Gene Name

PMS1 homolog2, mismatch repair system component

Synonyms

mismatch repair, DNA mismatch repair

MMRRC Submission

Accession Numbers

Essential gene?

Possibly non essential (E-score: 0.323) question?

Stock #

R9712 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

143909964-143933968 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 143914796 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Isoleucine to Threonine at position 177 (I177T)

Ref Sequence

ENSEMBL: ENSMUSP00000119875 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000031613] [ENSMUST00000100483] [ENSMUST00000110709] [ENSMUST00000148011] [ENSMUST00000164999]

AlphaFold

no structure available at present

Predicted Effect

probably benign
Transcript: ENSMUST00000031613

SMART Domains

Protein: ENSMUSP00000031613
Gene: ENSMUSG00000029610

Domain	Start	End	E-Value	Type
Pfam:AIMP2_LysRS_bd	1	44	8.3e-26	PFAM
low complexity region	133	142	N/A	INTRINSIC
Pfam:GST_C_3	231	308	2.5e-10	PFAM
Pfam:GST_C	242	310	5e-8	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000100483

SMART Domains

Protein: ENSMUSP00000098052
Gene: ENSMUSG00000029610

Domain	Start	End	E-Value	Type
low complexity region	93	102	N/A	INTRINSIC
Pfam:GST_C_3	185	268	1.1e-9	PFAM

Predicted Effect

probably damaging
Transcript: ENSMUST00000110709
AA Change: I177T

PolyPhen 2 Score 0.980 (Sensitivity: 0.75; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000106337
Gene: ENSMUSG00000079109
AA Change: I177T

Domain	Start	End	E-Value	Type
HATPase_c	30	165	3.77e-1	SMART
MutL_C	277	421	1.59e-36	SMART

Predicted Effect

probably damaging
Transcript: ENSMUST00000148011
AA Change: I177T

PolyPhen 2 Score 0.990 (Sensitivity: 0.72; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000119875
Gene: ENSMUSG00000079109
AA Change: I177T

Domain	Start	End	E-Value	Type
HATPase_c	30	165	3.77e-1	SMART
DNA_mis_repair	227	364	4.76e-41	SMART
MutL_C	675	819	1.59e-36	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000164999

SMART Domains

Protein: ENSMUSP00000133062
Gene: ENSMUSG00000079109

Domain	Start	End	E-Value	Type
DNA_mis_repair	1	70	4.47e-2	SMART

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.6%
20x: 98.6%

Validation Efficiency

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The protein encoded by this gene is a key component of the mismatch repair system that functions to correct DNA mismatches and small insertions and deletions that can occur during DNA replication and homologous recombination. This protein forms heterodimers with the gene product of the mutL homolog 1 (MLH1) gene to form the MutL-alpha heterodimer. The MutL-alpha heterodimer possesses an endonucleolytic activity that is activated following recognition of mismatches and insertion/deletion loops by the MutS-alpha and MutS-beta heterodimers, and is necessary for removal of the mismatched DNA. There is a DQHA(X)2E(X)4E motif found at the C-terminus of the protein encoded by this gene that forms part of the active site of the nuclease. Mutations in this gene have been associated with hereditary nonpolyposis colorectal cancer (HNPCC; also known as Lynch syndrome) and Turcot syndrome. [provided by RefSeq, Apr 2016]
PHENOTYPE: Homozygotes for targeted null mutations exhibit microsatellite instability and develop a high incidence of lymphomas with some sarcomas after 6 months of age. Mutant males are sterile, with impaired synapsis and only abnormal spermatozoa. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 84 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1810055G02Rik	A	T	19: 3,715,784 (GRCm38)	M20L	probably benign	Het
9430007A20Rik	C	T	4: 144,528,784 (GRCm38)	A258V	probably benign	Het
Abca8b	T	A	11: 109,942,337 (GRCm38)	D1241V	probably benign	Het
Adam20	G	A	8: 40,795,453 (GRCm38)	R200H	probably benign	Het
Adcy10	T	C	1: 165,513,112 (GRCm38)	F229L	probably damaging	Het
Adsl	A	T	15: 80,955,639 (GRCm38)	N126I	probably benign	Het
Ahnak	GATCTCTAT	GAT	19: 9,007,029 (GRCm38)		probably benign	Het
Ahnak	AGATCTC	A	19: 9,007,028 (GRCm38)		probably benign	Het
Aktip	G	A	8: 91,129,727 (GRCm38)	P41S	probably damaging	Het
Alkbh3	C	A	2: 93,980,973 (GRCm38)	R258L	probably damaging	Het
Arfgap3	A	G	15: 83,313,533 (GRCm38)	Y341H	probably benign	Het
Arhgef26	C	T	3: 62,423,613 (GRCm38)	L583F	probably damaging	Het
Arhgef40	T	C	14: 51,988,958 (GRCm38)	I153T	probably damaging	Het
Atp1a1	T	C	3: 101,591,441 (GRCm38)	S179G	probably benign	Het
Bok	T	C	1: 93,686,507 (GRCm38)	S21P	probably damaging	Het
C130060K24Rik	A	G	6: 65,456,140 (GRCm38)	I315V	probably benign	Het
Ccdc136	A	G	6: 29,417,442 (GRCm38)	E754G	probably benign	Het
Cers3	A	G	7: 66,773,630 (GRCm38)	K108E	probably benign	Het
Cmya5	T	C	13: 93,065,373 (GRCm38)		probably null	Het
Col19a1	T	C	1: 24,328,067 (GRCm38)	E478G	possibly damaging	Het
Colec10	T	A	15: 54,459,784 (GRCm38)	S134R	possibly damaging	Het
Ctnnb1	A	T	9: 120,955,829 (GRCm38)	I514F	probably damaging	Het
Cux1	C	T	5: 136,309,819 (GRCm38)	E664K	probably benign	Het
Dars	T	C	1: 128,405,462 (GRCm38)	Q75R	probably benign	Het
Disp1	T	A	1: 183,135,815 (GRCm38)	S16C	probably damaging	Het
Dnah7a	A	T	1: 53,559,140 (GRCm38)	V1412E	probably benign	Het
Ect2l	C	T	10: 18,168,434 (GRCm38)	V226I	probably benign	Het
Ep400	T	A	5: 110,756,643 (GRCm38)	H30L	unknown	Het
Ephx4	A	G	5: 107,419,781 (GRCm38)	I202V	probably benign	Het
Exoc3	A	T	13: 74,192,908 (GRCm38)	F259Y	probably damaging	Het
Ezr	T	C	17: 6,752,995 (GRCm38)	E229G	probably damaging	Het
Fat1	A	T	8: 45,017,380 (GRCm38)	I1472L	probably benign	Het
Fsd1l	T	G	4: 53,679,972 (GRCm38)	D223E	probably benign	Het
Gata6	A	T	18: 11,059,064 (GRCm38)	D377V	possibly damaging	Het
Gm12185	A	T	11: 48,907,389 (GRCm38)	M759K	probably benign	Het
Gm21994	C	T	2: 150,254,576 (GRCm38)	R311Q	probably benign	Het
Gm9922	C	T	14: 101,729,457 (GRCm38)	A120T	unknown	Het
Hectd4	A	T	5: 121,310,681 (GRCm38)	Y364F	probably benign	Het
Hnrnph1	A	G	11: 50,385,869 (GRCm38)	S465G	unknown	Het
Ifi204	T	C	1: 173,749,358 (GRCm38)	Y559C	probably damaging	Het
Ift88	T	C	14: 57,481,396 (GRCm38)	S613P	probably damaging	Het
Kif21a	G	T	15: 90,995,512 (GRCm38)	T191K	probably benign	Het
Kif21a	G	C	15: 90,985,325 (GRCm38)	A441G	probably damaging	Het
Lrit1	T	A	14: 37,060,127 (GRCm38)	C252*	probably null	Het
Ncbp1	T	A	4: 46,144,837 (GRCm38)	D29E	probably benign	Het
Nlrp10	A	T	7: 108,925,528 (GRCm38)	D248E	probably damaging	Het
Nphp4	T	G	4: 152,547,064 (GRCm38)	V807G	probably benign	Het
Nsd1	T	C	13: 55,246,043 (GRCm38)	S589P	possibly damaging	Het
Oas1b	T	A	5: 120,814,485 (GRCm38)	N80K	probably damaging	Het
Olfr1055	G	A	2: 86,347,239 (GRCm38)	H176Y	probably benign	Het
Olfr1135	A	T	2: 87,671,761 (GRCm38)	I202N	probably benign	Het
Oprk1	T	A	1: 5,598,873 (GRCm38)	C181S	probably damaging	Het
Oprl1	T	A	2: 181,718,419 (GRCm38)	N89K	probably damaging	Het
Pdcd11	A	G	19: 47,129,302 (GRCm38)	K1697E	probably damaging	Het
Pdp1	G	A	4: 11,961,607 (GRCm38)	H254Y	probably benign	Het
Pds5b	A	T	5: 150,805,663 (GRCm38)	D1419V	possibly damaging	Het
Per1	G	T	11: 69,100,649 (GRCm38)	G3V	probably benign	Het
Pex16	C	A	2: 92,376,643 (GRCm38)	N55K	probably damaging	Het
Phldb2	C	A	16: 45,774,977 (GRCm38)	L862F	probably benign	Het
Pld5	T	A	1: 175,964,006 (GRCm38)	D478V	probably benign	Het
Pou1f1	A	T	16: 65,529,872 (GRCm38)	E119D	probably benign	Het
Ppp2r1a	A	C	17: 20,958,796 (GRCm38)	E295A	probably damaging	Het
Rad51ap2	A	T	12: 11,457,592 (GRCm38)	N505I	possibly damaging	Het
Rasal3	A	C	17: 32,396,562 (GRCm38)	V434G	probably damaging	Het
Rasgrf2	C	T	13: 91,987,973 (GRCm38)	V6M		Het
Rwdd1	A	T	10: 34,001,156 (GRCm38)	D197E		Het
Scn11a	A	T	9: 119,790,010 (GRCm38)	C755*	probably null	Het
Skil	T	C	3: 31,116,860 (GRCm38)	S443P	probably benign	Het
Slc12a6	T	C	2: 112,356,472 (GRCm38)	C939R	probably damaging	Het
Slc25a36	A	G	9: 97,079,177 (GRCm38)	S269P	probably benign	Het
Srrm4	T	A	5: 116,482,393 (GRCm38)	H92L	unknown	Het
Styk1	CTCTTCATGATTTTCTT	CTCTT	6: 131,301,649 (GRCm38)		probably benign	Het
Tbc1d4	A	T	14: 101,507,410 (GRCm38)	V260E	probably benign	Het
Tbc1d8	T	C	1: 39,385,232 (GRCm38)	N593D	probably damaging	Het
Trex1	C	A	9: 109,058,737 (GRCm38)	R62L	probably damaging	Het
Trpm3	A	T	19: 22,715,352 (GRCm38)	D269V	possibly damaging	Het
Trpv4	G	T	5: 114,633,150 (GRCm38)	Y439*	probably null	Het
Ttn	G	A	2: 76,734,248 (GRCm38)	T28515I	probably damaging	Het
Ucn2	G	A	9: 108,986,503 (GRCm38)	G111D	probably damaging	Het
Uhrf2	A	G	19: 30,056,481 (GRCm38)	I212V	possibly damaging	Het
Usp24	T	A	4: 106,347,367 (GRCm38)	M261K	probably benign	Het
Vmn1r235	A	T	17: 21,261,698 (GRCm38)	D95V	probably benign	Het
Vwf	G	A	6: 125,624,573 (GRCm38)	R826Q		Het
Zfp28	T	C	7: 6,393,879 (GRCm38)	C438R	probably damaging	Het

Other mutations in Pms2

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01893:Pms2	APN	5	143,923,519 (GRCm38)	missense	probably damaging	1.00
IGL02009:Pms2	APN	5	143,925,764 (GRCm38)	missense	probably benign	0.42
IGL02801:Pms2	APN	5	143,925,835 (GRCm38)	missense	probably benign	0.06
P0047:Pms2	UTSW	5	143,919,598 (GRCm38)	missense	probably damaging	1.00
R1367:Pms2	UTSW	5	143,925,913 (GRCm38)	missense	probably damaging	1.00
R1422:Pms2	UTSW	5	143,913,705 (GRCm38)	missense	probably damaging	1.00
R1854:Pms2	UTSW	5	143,925,896 (GRCm38)	missense	probably benign	0.08
R1997:Pms2	UTSW	5	143,913,700 (GRCm38)	missense	probably damaging	1.00
R2248:Pms2	UTSW	5	143,916,506 (GRCm38)	missense	probably damaging	1.00
R2873:Pms2	UTSW	5	143,911,914 (GRCm38)	splice site	probably benign
R4072:Pms2	UTSW	5	143,929,001 (GRCm38)	missense	probably damaging	0.99
R4082:Pms2	UTSW	5	143,931,019 (GRCm38)	missense	probably damaging	1.00
R4358:Pms2	UTSW	5	143,925,926 (GRCm38)	missense	probably damaging	1.00
R5100:Pms2	UTSW	5	143,928,188 (GRCm38)	missense	probably damaging	1.00
R5101:Pms2	UTSW	5	143,928,188 (GRCm38)	missense	probably damaging	1.00
R5228:Pms2	UTSW	5	143,923,597 (GRCm38)	missense	probably damaging	0.99
R5484:Pms2	UTSW	5	143,928,125 (GRCm38)	missense	probably damaging	1.00
R6310:Pms2	UTSW	5	143,923,583 (GRCm38)	missense	probably benign	0.06
R6331:Pms2	UTSW	5	143,914,633 (GRCm38)	missense	possibly damaging	0.94
R6567:Pms2	UTSW	5	143,928,968 (GRCm38)	missense	probably damaging	0.99
R6718:Pms2	UTSW	5	143,923,489 (GRCm38)	missense	probably damaging	0.98
R6747:Pms2	UTSW	5	143,925,419 (GRCm38)	missense	probably benign	0.02
R6980:Pms2	UTSW	5	143,912,024 (GRCm38)	missense	probably benign	0.21
R7207:Pms2	UTSW	5	143,913,634 (GRCm38)	missense	probably damaging	1.00
R7349:Pms2	UTSW	5	143,925,836 (GRCm38)	missense	probably benign	0.11
R7657:Pms2	UTSW	5	143,919,539 (GRCm38)	missense	possibly damaging	0.93
R7820:Pms2	UTSW	5	143,914,633 (GRCm38)	missense	possibly damaging	0.80
R7980:Pms2	UTSW	5	143,931,091 (GRCm38)	missense	probably damaging	1.00
R8213:Pms2	UTSW	5	143,914,771 (GRCm38)	missense	probably damaging	1.00
R8534:Pms2	UTSW	5	143,923,627 (GRCm38)	missense	probably benign	0.16
R9021:Pms2	UTSW	5	143,925,926 (GRCm38)	missense	probably damaging	1.00
R9218:Pms2	UTSW	5	143,931,127 (GRCm38)	missense	probably benign
R9494:Pms2	UTSW	5	143,916,396 (GRCm38)	missense	probably damaging	1.00
R9614:Pms2	UTSW	5	143,917,602 (GRCm38)	missense	probably benign	0.01
X0064:Pms2	UTSW	5	143,916,466 (GRCm38)	nonsense	probably null

Predicted Primers

PCR Primer
(F):5'- TATATCTACCTGCCACGGGTC -3'
(R):5'- TTGACAACCGCTGTGCCATC -3'

Sequencing Primer
(F):5'- TCTGCAAGCGTTGGGACTC -3'
(R):5'- TGGAACTCACTCTGTAGACCAGG -3'

Posted On

2022-10-06