Mutagenetix > Incidental Mutation

Incidental Mutation 'R1874:Pms1'

210993

Institutional Source

Beutler Lab

Gene Symbol

Pms1

Ensembl Gene

ENSMUSG00000026098

Gene Name

PMS1 homolog 1, mismatch repair system component

Synonyms

MMRRC Submission

039896-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R1874 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

53228346-53336177 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to T at 53246392 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Asparagine to Lysine at position 382 (N382K)

Ref Sequence

ENSEMBL: ENSMUSP00000119632 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000027267] [ENSMUST00000135246]

AlphaFold

Q8K119

Predicted Effect

probably benign
Transcript: ENSMUST00000027267
AA Change: N382K

PolyPhen 2 Score 0.102 (Sensitivity: 0.93; Specificity: 0.86)

SMART Domains

Protein: ENSMUSP00000027267
Gene: ENSMUSG00000026098
AA Change: N382K

Domain	Start	End	E-Value	Type
HATPase_c	16	151	3.84e-1	SMART
DNA_mis_repair	210	338	2.46e-25	SMART
low complexity region	457	474	N/A	INTRINSIC
HMG	557	627	1.42e-17	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000135246
AA Change: N382K

PolyPhen 2 Score 0.163 (Sensitivity: 0.92; Specificity: 0.87)

SMART Domains

Protein: ENSMUSP00000119632
Gene: ENSMUSG00000026098
AA Change: N382K

Domain	Start	End	E-Value	Type
HATPase_c	16	151	3.84e-1	SMART
DNA_mis_repair	210	338	2.46e-25	SMART
low complexity region	457	474	N/A	INTRINSIC
HMG	557	627	1.42e-17	SMART

Meta Mutation Damage Score

0.3601

Coding Region Coverage

1x: 97.5%
3x: 97.0%
10x: 95.8%
20x: 94.1%

Validation Efficiency

96% (105/109)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a protein belonging to the DNA mismatch repair mutL/hexB family. This protein is thought to be involved in the repair of DNA mismatches, and it can form heterodimers with MLH1, a known DNA mismatch repair protein. Mutations in this gene cause hereditary nonpolyposis colorectal cancer type 3 (HNPCC3) either alone or in combination with mutations in other genes involved in the HNPCC phenotype, which is also known as Lynch syndrome. [provided by RefSeq, Jul 2008]
PHENOTYPE: Homozygotes for a targeted null mutation exhibit a modest increase in DNA mismatch repair errors, primarily single base pair substitutions. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 104 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
AA986860	A	G	1: 130,670,428 (GRCm39)	S217G	probably benign	Het
Adrb3	C	A	8: 27,717,591 (GRCm39)	R286L	probably damaging	Het
Akap11	T	A	14: 78,749,306 (GRCm39)	D1027V	probably benign	Het
Ank3	A	T	10: 69,733,913 (GRCm39)	I726F	probably damaging	Het
Ankmy2	T	A	12: 36,215,930 (GRCm39)	D43E	possibly damaging	Het
Ankrd34b	A	G	13: 92,576,064 (GRCm39)	D432G	probably damaging	Het
Ano3	A	C	2: 110,715,217 (GRCm39)	S74A	probably benign	Het
B4galnt4	T	A	7: 140,650,439 (GRCm39)	S769T	probably damaging	Het
Bicral	T	A	17: 47,136,104 (GRCm39)	T369S	probably benign	Het
Blm	A	G	7: 80,147,166 (GRCm39)	L738P	probably damaging	Het
Bpifb3	A	G	2: 153,767,760 (GRCm39)	T278A	probably benign	Het
Bpifb5	A	G	2: 154,069,122 (GRCm39)		probably benign	Het
Brd8	G	C	18: 34,743,527 (GRCm39)	P266R	probably damaging	Het
Btaf1	A	T	19: 36,957,983 (GRCm39)	M587L	probably benign	Het
Casz1	C	G	4: 149,027,668 (GRCm39)	T1015S	probably damaging	Het
Cdh23	A	G	10: 60,272,597 (GRCm39)	I524T	possibly damaging	Het
Celsr3	T	C	9: 108,713,037 (GRCm39)	V1825A	probably benign	Het
Cenpf	A	G	1: 189,416,013 (GRCm39)	L104P	probably damaging	Het
Clasp1	G	T	1: 118,528,315 (GRCm39)		probably null	Het
Coprs	A	G	8: 13,935,112 (GRCm39)	W148R	probably damaging	Het
Cpne1	A	G	2: 155,920,302 (GRCm39)	S168P	probably damaging	Het
Cpxm2	T	C	7: 131,661,563 (GRCm39)	Y408C	probably damaging	Het
Ctnna3	A	G	10: 63,339,886 (GRCm39)	E24G	possibly damaging	Het
Cubn	T	A	2: 13,327,813 (GRCm39)	S2671C	probably damaging	Het
Cyp4f39	T	A	17: 32,702,298 (GRCm39)	F265Y	probably damaging	Het
Dgkq	C	A	5: 108,808,461 (GRCm39)	R34L	probably benign	Het
Dnajc7	C	T	11: 100,490,139 (GRCm39)		probably benign	Het
Eml6	T	G	11: 29,781,136 (GRCm39)	D632A	probably damaging	Het
Fbxl18	G	A	5: 142,871,978 (GRCm39)	A419V	probably damaging	Het
Fbxw22	A	T	9: 109,214,179 (GRCm39)	C212*	probably null	Het
Ffar2	A	G	7: 30,518,839 (GRCm39)		probably null	Het
Fga	A	T	3: 82,940,028 (GRCm39)	T561S	probably damaging	Het
Fry	A	G	5: 150,269,386 (GRCm39)	Y159C	probably damaging	Het
Gal3st1	A	G	11: 3,948,231 (GRCm39)	Y146C	probably damaging	Het
Gapvd1	A	T	2: 34,596,033 (GRCm39)	H788Q	probably damaging	Het
Gimap7	G	A	6: 48,700,449 (GRCm39)	V12I	possibly damaging	Het
Gli2	C	A	1: 118,929,779 (GRCm39)	A43S	possibly damaging	Het
Gm15446	T	C	5: 110,090,419 (GRCm39)	F224L	probably damaging	Het
Gm21738	C	T	14: 19,418,824 (GRCm38)	V35I	possibly damaging	Het
Grhl1	T	C	12: 24,636,155 (GRCm39)		probably benign	Het
Grk6	T	C	13: 55,598,086 (GRCm39)	Y53H	probably damaging	Het
Hcar1	C	T	5: 124,017,328 (GRCm39)	R121K	probably damaging	Het
Hmcn1	A	C	1: 150,596,446 (GRCm39)	S1797A	probably damaging	Het
Hsd17b7	A	T	1: 169,783,562 (GRCm39)	L282Q	possibly damaging	Het
Irs1	TTCTCTGAGTGGCCACAGCGTCT	TTCT	1: 82,267,574 (GRCm39)		probably null	Het
Kif1b	C	T	4: 149,272,089 (GRCm39)	V1571I	probably benign	Het
Lpl	T	A	8: 69,349,271 (GRCm39)	C266S	probably damaging	Het
Mag	G	A	7: 30,608,476 (GRCm39)	H213Y	probably benign	Het
Mansc4	T	G	6: 146,976,688 (GRCm39)	R309S	probably benign	Het
Mlh3	A	G	12: 85,284,287 (GRCm39)		probably null	Het
Mndal	G	A	1: 173,687,933 (GRCm39)		probably benign	Het
Mrgpra2b	T	A	7: 47,113,742 (GRCm39)	E330V	probably damaging	Het
Myh3	A	G	11: 66,984,005 (GRCm39)	I990V	probably benign	Het
Myoz2	A	T	3: 122,819,765 (GRCm39)	S65T	probably damaging	Het
Naa16	T	C	14: 79,593,183 (GRCm39)	E463G	possibly damaging	Het
Nadsyn1	A	G	7: 143,351,581 (GRCm39)	F684S	probably damaging	Het
Notch1	T	C	2: 26,371,591 (GRCm39)	E286G	possibly damaging	Het
Nynrin	A	T	14: 56,100,950 (GRCm39)	I247L	probably benign	Het
Oprm1	A	G	10: 6,739,035 (GRCm39)	H54R	probably benign	Het
Or10g6	T	A	9: 39,934,151 (GRCm39)	I154N	possibly damaging	Het
Or2n1d	C	T	17: 38,646,860 (GRCm39)	P271S	probably damaging	Het
Or51a43	T	C	7: 103,717,336 (GRCm39)	I301V	probably null	Het
P4hb	C	T	11: 120,452,992 (GRCm39)	D483N	probably benign	Het
Pak1	T	C	7: 97,520,787 (GRCm39)	S149P	probably benign	Het
Pars2	T	C	4: 106,510,913 (GRCm39)	F232L	possibly damaging	Het
Pih1d2	A	G	9: 50,532,245 (GRCm39)	M88V	possibly damaging	Het
Pnliprp2	G	T	19: 58,751,821 (GRCm39)	V189L	probably benign	Het
Pole	G	A	5: 110,471,530 (GRCm39)	V1425M	possibly damaging	Het
Pot1b	T	A	17: 55,961,805 (GRCm39)	Q591L	probably benign	Het
Ppp1r9a	C	T	6: 4,906,348 (GRCm39)	T301M	possibly damaging	Het
Psg21	T	C	7: 18,384,741 (GRCm39)	E335G	probably benign	Het
Ptpru	T	A	4: 131,497,066 (GRCm39)	M1416L	probably benign	Het
Pxn	T	C	5: 115,683,049 (GRCm39)	V117A	probably damaging	Het
Qsox1	C	T	1: 155,688,385 (GRCm39)	R54H	possibly damaging	Het
Rad1	A	G	15: 10,488,092 (GRCm39)	E42G	probably damaging	Het
Rpp14	A	G	14: 8,090,145 (GRCm38)	Y23C	probably benign	Het
Sdk2	C	T	11: 113,725,782 (GRCm39)	V1156I	probably benign	Het
Serpina3j	G	T	12: 104,285,958 (GRCm39)	R371L	probably benign	Het
Serpinb9d	T	A	13: 33,381,946 (GRCm39)		probably null	Het
Sirt5	C	T	13: 43,524,267 (GRCm39)	S13F	possibly damaging	Het
Slc6a7	T	A	18: 61,134,470 (GRCm39)		probably benign	Het
Slx4	A	G	16: 3,804,712 (GRCm39)	S701P	probably benign	Het
Snx29	A	G	16: 11,185,545 (GRCm39)	T43A	probably benign	Het
Speg	T	C	1: 75,400,550 (GRCm39)	V2570A	probably benign	Het
Srrm4	T	A	5: 116,591,565 (GRCm39)		probably benign	Het
Stk32a	A	G	18: 43,394,381 (GRCm39)	Y110C	probably damaging	Het
Tbc1d31	G	A	15: 57,779,506 (GRCm39)	G73E	probably benign	Het
Thsd7a	A	T	6: 12,555,434 (GRCm39)	I150N	possibly damaging	Het
Tjp1	A	T	7: 64,969,001 (GRCm39)	D699E	probably damaging	Het
Tmem143	A	G	7: 45,565,988 (GRCm39)	D437G	possibly damaging	Het
Tmem45a2	A	G	16: 56,867,447 (GRCm39)	Y85H	possibly damaging	Het
Tmem45b	T	A	9: 31,340,383 (GRCm39)	T7S	probably damaging	Het
Tut4	T	A	4: 108,407,922 (GRCm39)	V1397D	probably damaging	Het
Ube4b	A	G	4: 149,432,428 (GRCm39)	L832P	probably damaging	Het
Ugp2	G	T	11: 21,279,048 (GRCm39)	F379L	probably damaging	Het
Ugt3a1	A	T	15: 9,365,437 (GRCm39)	D350V	probably damaging	Het
Vmn2r8	T	A	5: 108,950,284 (GRCm39)	T188S	possibly damaging	Het
Vwa7	C	G	17: 35,236,088 (GRCm39)	P14R	probably benign	Het
Vwc2	C	A	11: 11,211,495 (GRCm39)	T317K	probably damaging	Het
Vwf	A	T	6: 125,605,335 (GRCm39)	Q906L	probably benign	Het
Wdr49	A	G	3: 75,336,654 (GRCm39)	V351A	probably damaging	Het
Wdr7	A	G	18: 63,861,575 (GRCm39)	S196G	probably benign	Het
Xkr6	C	A	14: 64,035,745 (GRCm39)	A26E	unknown	Het
Zfp955b	T	C	17: 33,524,427 (GRCm39)	I47V	probably benign	Het

Other mutations in Pms1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00494:Pms1	APN	1	53,245,715 (GRCm39)	splice site	probably benign
IGL00937:Pms1	APN	1	53,314,410 (GRCm39)	missense	possibly damaging	0.74
IGL01505:Pms1	APN	1	53,246,130 (GRCm39)	missense	probably benign
IGL02109:Pms1	APN	1	53,246,568 (GRCm39)	missense	probably damaging	0.96
IGL02245:Pms1	APN	1	53,246,519 (GRCm39)	missense	probably damaging	1.00
IGL02273:Pms1	APN	1	53,247,156 (GRCm39)	missense	probably damaging	1.00
IGL02339:Pms1	APN	1	53,314,324 (GRCm39)	missense	possibly damaging	0.78
R0157:Pms1	UTSW	1	53,234,196 (GRCm39)	nonsense	probably null
R0530:Pms1	UTSW	1	53,235,972 (GRCm39)	splice site	probably null
R1398:Pms1	UTSW	1	53,246,435 (GRCm39)	missense	possibly damaging	0.88
R1817:Pms1	UTSW	1	53,246,128 (GRCm39)	missense	probably benign	0.02
R1831:Pms1	UTSW	1	53,246,370 (GRCm39)	missense	probably benign	0.00
R1838:Pms1	UTSW	1	53,231,257 (GRCm39)	critical splice donor site	probably null
R1867:Pms1	UTSW	1	53,228,546 (GRCm39)	missense	probably benign	0.36
R1939:Pms1	UTSW	1	53,236,135 (GRCm39)	missense	probably damaging	1.00
R1991:Pms1	UTSW	1	53,321,201 (GRCm39)	missense	probably damaging	1.00
R1993:Pms1	UTSW	1	53,234,174 (GRCm39)	missense	probably benign
R1995:Pms1	UTSW	1	53,234,174 (GRCm39)	missense	probably benign
R2049:Pms1	UTSW	1	53,321,147 (GRCm39)	missense	probably damaging	0.99
R2058:Pms1	UTSW	1	53,314,327 (GRCm39)	missense	probably benign	0.00
R2140:Pms1	UTSW	1	53,321,147 (GRCm39)	missense	probably damaging	0.99
R4078:Pms1	UTSW	1	53,306,948 (GRCm39)	splice site	probably null
R4608:Pms1	UTSW	1	53,234,097 (GRCm39)	missense	possibly damaging	0.80
R4668:Pms1	UTSW	1	53,228,633 (GRCm39)	nonsense	probably null
R5164:Pms1	UTSW	1	53,246,799 (GRCm39)	missense	probably damaging	0.99
R5200:Pms1	UTSW	1	53,245,916 (GRCm39)	missense	probably benign	0.00
R5397:Pms1	UTSW	1	53,231,279 (GRCm39)	nonsense	probably null
R5745:Pms1	UTSW	1	53,246,861 (GRCm39)	nonsense	probably null
R6440:Pms1	UTSW	1	53,234,180 (GRCm39)	missense	probably damaging	0.98
R6445:Pms1	UTSW	1	53,231,353 (GRCm39)	missense	possibly damaging	0.77
R6802:Pms1	UTSW	1	53,245,951 (GRCm39)	missense	probably benign	0.06
R6975:Pms1	UTSW	1	53,228,590 (GRCm39)	missense	probably damaging	0.99
R7020:Pms1	UTSW	1	53,228,541 (GRCm39)	missense	probably damaging	1.00
R7037:Pms1	UTSW	1	53,246,770 (GRCm39)	missense	possibly damaging	0.95
R7199:Pms1	UTSW	1	53,295,889 (GRCm39)	missense	probably benign	0.02
R7417:Pms1	UTSW	1	53,236,231 (GRCm39)	missense	probably benign	0.00
R7587:Pms1	UTSW	1	53,246,475 (GRCm39)	missense	probably benign	0.00
R7716:Pms1	UTSW	1	53,246,767 (GRCm39)	missense	probably damaging	1.00
R8178:Pms1	UTSW	1	53,246,505 (GRCm39)	missense	probably benign	0.00
R8336:Pms1	UTSW	1	53,245,985 (GRCm39)	missense	probably benign
R8399:Pms1	UTSW	1	53,307,091 (GRCm39)	critical splice acceptor site	probably null
R8692:Pms1	UTSW	1	53,246,052 (GRCm39)	missense	probably benign
R8736:Pms1	UTSW	1	53,307,053 (GRCm39)	missense	possibly damaging	0.63
R8738:Pms1	UTSW	1	53,321,195 (GRCm39)	missense	possibly damaging	0.67
R8751:Pms1	UTSW	1	53,231,269 (GRCm39)	missense	probably benign	0.01
R9102:Pms1	UTSW	1	53,307,021 (GRCm39)	missense	probably benign	0.11
R9294:Pms1	UTSW	1	53,247,216 (GRCm39)	missense	probably benign
R9648:Pms1	UTSW	1	53,314,284 (GRCm39)	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- GGATGTGCTCCATAGAACCTAC -3'
(R):5'- AGATATTGCCCCTTTCACAGTATCC -3'

Sequencing Primer
(F):5'- TGTGCTCCATAGAACCTACAGAATG -3'
(R):5'- TCACAGTATCCCTCCTAATACTTG -3'

Posted On

2014-06-30