Mutagenetix > Incidental Mutation

Incidental Mutation 'R1398:Pms1'

160210

Institutional Source

Beutler Lab

Gene Symbol

Pms1

Ensembl Gene

ENSMUSG00000026098

Gene Name

PMS1 homolog 1, mismatch repair system component

Synonyms

MMRRC Submission

039460-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R1398 (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 53246435 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Valine to Glutamic Acid at position 368 (V368E)

Ref Sequence

ENSEMBL: ENSMUSP00000119632 (fasta)

Gene Model

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

AlphaFold

Q8K119

Predicted Effect

possibly damaging
Transcript: ENSMUST00000027267
AA Change: V368E

PolyPhen 2 Score 0.881 (Sensitivity: 0.82; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000027267
Gene: ENSMUSG00000026098
AA Change: V368E

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

possibly damaging
Transcript: ENSMUST00000135246
AA Change: V368E

PolyPhen 2 Score 0.881 (Sensitivity: 0.82; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000119632
Gene: ENSMUSG00000026098
AA Change: V368E

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

0.1853

Coding Region Coverage

1x: 99.0%
3x: 98.1%
10x: 95.6%
20x: 90.7%

Validation Efficiency

96% (75/78)

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: 74 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abca17	T	C	17: 24,547,511 (GRCm39)	K288E	probably damaging	Het
Aldh3a2	T	C	11: 61,147,562 (GRCm39)		probably null	Het
Anks1b	A	G	10: 89,885,891 (GRCm39)	T196A	probably damaging	Het
Anks6	T	A	4: 47,044,926 (GRCm39)	T327S	possibly damaging	Het
Bdh2	T	C	3: 135,001,057 (GRCm39)		probably benign	Het
C4b	T	A	17: 34,949,693 (GRCm39)		probably benign	Het
Cacna2d1	G	A	5: 16,562,764 (GRCm39)	V847I	possibly damaging	Het
Cadps	G	T	14: 12,449,822 (GRCm38)	T1129K	probably damaging	Het
Cdc45	A	G	16: 18,600,721 (GRCm39)		probably benign	Het
Cep63	A	T	9: 102,480,285 (GRCm39)		probably benign	Het
Chil4	T	A	3: 106,126,825 (GRCm39)		probably null	Het
Cnot11	A	G	1: 39,584,261 (GRCm39)	R478G	probably damaging	Het
Cyp2c67	A	G	19: 39,627,069 (GRCm39)	S254P	probably damaging	Het
Dnah11	T	A	12: 118,020,841 (GRCm39)	K87*	probably null	Het
Dpy19l2	T	A	9: 24,492,559 (GRCm39)		probably benign	Het
Dsc1	A	T	18: 20,221,393 (GRCm39)	I694N	probably damaging	Het
Ehd4	A	T	2: 119,958,081 (GRCm39)	I168K	probably benign	Het
Eif4e	A	T	3: 138,252,136 (GRCm39)	N25Y	probably damaging	Het
Elapor2	A	G	5: 9,430,297 (GRCm39)	Y69C	probably damaging	Het
Eme2	G	A	17: 25,111,892 (GRCm39)	S263F	probably damaging	Het
Fgfrl1	T	A	5: 108,854,147 (GRCm39)		probably benign	Het
Fhip2a	T	A	19: 57,361,358 (GRCm39)		probably benign	Het
Gm3159	T	A	14: 4,398,586 (GRCm38)	Y92*	probably null	Het
Gm4922	T	A	10: 18,659,496 (GRCm39)	S409C	possibly damaging	Het
Gmcl1	G	A	6: 86,691,244 (GRCm39)		probably benign	Het
Grsf1	A	G	5: 88,813,706 (GRCm39)	Y231H	probably benign	Het
Heatr4	T	A	12: 84,014,395 (GRCm39)	H614L	possibly damaging	Het
Hoxa13	C	G	6: 52,260,647 (GRCm38)		probably benign	Het
Hoxa13	G	C	6: 52,260,648 (GRCm38)		probably benign	Het
Isg20l2	C	A	3: 87,846,061 (GRCm39)	L325I	probably benign	Het
Kalrn	A	G	16: 34,033,190 (GRCm39)	Y879H	probably damaging	Het
Kcnk10	C	A	12: 98,402,485 (GRCm39)	W318L	probably damaging	Het
Kctd1	T	C	18: 15,195,654 (GRCm39)	E323G	possibly damaging	Het
Kif4	G	T	X: 99,732,703 (GRCm39)	A492S	probably benign	Het
Krtap4-1	T	C	11: 99,518,558 (GRCm39)	T151A	unknown	Het
Ldlr	A	T	9: 21,650,838 (GRCm39)	Q449L	probably benign	Het
Lepr	T	A	4: 101,649,216 (GRCm39)	D872E	probably damaging	Het
Lgals12	C	T	19: 7,581,322 (GRCm39)		probably benign	Het
Lrig3	C	T	10: 125,838,957 (GRCm39)	P488L	probably benign	Het
Lrrc4b	A	C	7: 44,111,876 (GRCm39)	I583L	probably benign	Het
Lyst	T	C	13: 13,915,121 (GRCm39)	S3272P	possibly damaging	Het
Marchf2	T	C	17: 33,915,096 (GRCm39)	H166R	probably damaging	Het
Mtbp	C	A	15: 55,440,933 (GRCm39)	Y373*	probably null	Het
Myh2	C	T	11: 67,076,113 (GRCm39)	H767Y	probably benign	Het
Ncam1	G	A	9: 49,428,889 (GRCm39)		probably benign	Het
Neb	T	A	2: 52,179,658 (GRCm39)	N1282Y	probably damaging	Het
Nectin3	A	G	16: 46,269,119 (GRCm39)	Y428H	possibly damaging	Het
Nrros	A	T	16: 31,961,962 (GRCm39)	I649N	probably damaging	Het
Nvl	A	T	1: 180,924,691 (GRCm39)		probably benign	Het
Or5p70	T	A	7: 107,994,708 (GRCm39)	V127E	probably damaging	Het
Polq	T	A	16: 36,882,857 (GRCm39)	S1674T	possibly damaging	Het
Ppp1r21	T	C	17: 88,850,307 (GRCm39)	V31A	probably damaging	Het
Rev3l	T	A	10: 39,697,579 (GRCm39)	V692E	probably benign	Het
Robo4	T	C	9: 37,319,372 (GRCm39)		probably null	Het
Rps6kc1	T	C	1: 190,532,212 (GRCm39)	I597V	probably damaging	Het
Rtel1	T	A	2: 180,977,658 (GRCm39)		probably null	Het
Scn9a	A	G	2: 66,314,930 (GRCm39)	M1587T	probably benign	Het
Sec31b	T	A	19: 44,512,104 (GRCm39)	I597F	probably benign	Het
Skint5	T	C	4: 113,636,268 (GRCm39)	N650S	unknown	Het
Slc22a28	G	T	19: 8,107,566 (GRCm39)	S167*	probably null	Het
Slfn1	T	A	11: 83,011,968 (GRCm39)	M28K	probably damaging	Het
Smc6	T	C	12: 11,321,880 (GRCm39)		probably benign	Het
Sox8	T	C	17: 25,786,857 (GRCm39)	H282R	probably benign	Het
Spata31e2	G	T	1: 26,724,422 (GRCm39)	Q253K	possibly damaging	Het
Syngr3	C	A	17: 24,905,414 (GRCm39)	V161L	probably benign	Het
Trak1	C	T	9: 121,283,425 (GRCm39)	S397F	probably damaging	Het
Uso1	C	T	5: 92,329,327 (GRCm39)	A405V	probably benign	Het
Uvrag	G	T	7: 98,715,027 (GRCm39)	Y190*	probably null	Het
Vps13d	A	T	4: 144,826,553 (GRCm39)	L1726Q	probably null	Het
Vwf	A	T	6: 125,580,420 (GRCm39)	Q556L	probably benign	Het
Wdr70	T	A	15: 8,065,325 (GRCm39)	M246L	probably benign	Het
Yipf3	T	C	17: 46,562,372 (GRCm39)	F285S	probably damaging	Het
Zdhhc13	G	A	7: 48,476,621 (GRCm39)	G579R	probably damaging	Het
Zdhhc18	G	C	4: 133,354,608 (GRCm39)	F125L	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
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
R1874:Pms1	UTSW	1	53,246,392 (GRCm39)	missense	probably benign	0.16
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'- TCGTCTGCACAGATTTCCAGAGC -3'
(R):5'- AAGTGCCTAAAGGAGTCTACCCGC -3'

Sequencing Primer
(F):5'- TGGATGTGCTCCATAGAACC -3'
(R):5'- AAAGGAGTCTACCCGCTTGTATC -3'

Posted On

2014-03-14