Mutagenetix > Incidental Mutations

Incidental Mutation 'R2022:Frem1'

224098

Institutional Source

Beutler Lab

Gene Symbol

Frem1

Ensembl Gene

ENSMUSG00000059049

Gene Name

Fras1 related extracellular matrix protein 1

Synonyms

eyes2, heb, eye, crf11, QBRICK

MMRRC Submission

040031-MU

Accession Numbers

Is this an essential gene?

Possibly essential (E-score: 0.732) question?

Stock #

R2022 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

82897920-83052339 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

G to T at 82913558 bp

Zygosity

Heterozygous

Amino Acid Change

Threonine to Lysine at position 1988 (T1988K)

Ref Sequence

ENSEMBL: ENSMUSP00000102849 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000071708] [ENSMUST00000107230] [ENSMUST00000170248]

Predicted Effect

probably benign
Transcript: ENSMUST00000071708
AA Change: T2007K

PolyPhen 2 Score 0.023 (Sensitivity: 0.95; Specificity: 0.81)

SMART Domains

Protein: ENSMUSP00000071627
Gene: ENSMUSG00000059049
AA Change: T2007K

Domain	Start	End	E-Value	Type
signal peptide	1	29	N/A	INTRINSIC
Pfam:Cadherin_3	364	508	1.7e-37	PFAM
Pfam:Cadherin_3	509	623	3.7e-18	PFAM
Pfam:Cadherin_3	592	709	8.4e-16	PFAM
Pfam:Cadherin_3	746	894	4.8e-26	PFAM
Pfam:Cadherin_3	863	1009	2.8e-30	PFAM
Pfam:Cadherin_3	1024	1115	6.4e-13	PFAM
Pfam:Cadherin_3	1119	1252	1.4e-17	PFAM
Pfam:Cadherin_3	1243	1393	8.2e-35	PFAM
Pfam:Cadherin_3	1378	1506	2e-22	PFAM
Pfam:Cadherin_3	1506	1616	1e-29	PFAM
Pfam:Cadherin_3	1617	1744	1.5e-14	PFAM
Pfam:Calx-beta	1749	1848	2.6e-10	PFAM
low complexity region	1894	1910	N/A	INTRINSIC
CLECT	2065	2188	2.25e-27	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000107230
AA Change: T1988K

PolyPhen 2 Score 0.023 (Sensitivity: 0.95; Specificity: 0.81)

SMART Domains

Protein: ENSMUSP00000102849
Gene: ENSMUSG00000059049
AA Change: T1988K

Domain	Start	End	E-Value	Type
signal peptide	1	29	N/A	INTRINSIC
internal_repeat_1	296	967	9.01e-39	PROSPERO
internal_repeat_1	1026	1705	9.01e-39	PROSPERO
Pfam:Calx-beta	1730	1829	6.7e-10	PFAM
low complexity region	1875	1891	N/A	INTRINSIC
CLECT	2046	2169	2.25e-27	SMART

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000130889

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000133610

Predicted Effect

probably benign
Transcript: ENSMUST00000170248
AA Change: T1989K

PolyPhen 2 Score 0.003 (Sensitivity: 0.98; Specificity: 0.44)

SMART Domains

Protein: ENSMUSP00000125809
Gene: ENSMUSG00000059049
AA Change: T1989K

Domain	Start	End	E-Value	Type
signal peptide	1	29	N/A	INTRINSIC
Pfam:Cadherin_3	365	509	1.3e-37	PFAM
Pfam:Cadherin_3	510	623	4.5e-18	PFAM
Pfam:Cadherin_3	593	711	6.1e-16	PFAM
Pfam:Cadherin_3	728	876	2.7e-27	PFAM
Pfam:Cadherin_3	845	991	2.1e-30	PFAM
Pfam:Cadherin_3	1006	1097	4.8e-13	PFAM
Pfam:Cadherin_3	1101	1234	1e-17	PFAM
Pfam:Cadherin_3	1225	1375	6.1e-35	PFAM
Pfam:Cadherin_3	1360	1488	1.5e-22	PFAM
Pfam:Cadherin_3	1488	1598	7.5e-30	PFAM
Pfam:Cadherin_3	1599	1726	1.1e-14	PFAM
Pfam:Calx-beta	1731	1830	6.4e-10	PFAM
low complexity region	1876	1892	N/A	INTRINSIC
CLECT	2047	2170	2.25e-27	SMART

Meta Mutation Damage Score

0.0671

Coding Region Coverage

1x: 99.2%
3x: 98.6%
10x: 97.1%
20x: 94.7%

Validation Efficiency

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a basement membrane protein that may play a role in craniofacial and renal development. Mutations in this gene have been associated with bifid nose with or without anorectal and renal anomalies. Alternatively spliced transcript variants encoding different isoforms have been described. PubMed ID 19940113 describes one such variant that initiates transcription within a distinct, internal exon; the resulting shorter isoform (named Toll-like/interleukin-1 receptor regulator, TILRR) is suggested to be a co-receptor of the interleukin 1 receptor family and may regulate receptor function and Toll-like receptor/interleukin 1 receptor signal transduction, contributing to the control of inflammatory response activation. [provided by RefSeq, Apr 2011]
PHENOTYPE: Homozygous mutation of this gene results in subepidermal blistering, cryptophthalmos, syndactyly, and renal agenesis. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 89 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Akr1cl	T	A	1: 65,014,698	Y271F	probably benign	Het
Asnsd1	A	G	1: 53,347,227	S414P	possibly damaging	Het
Atp12a	T	A	14: 56,365,282	M1K	probably null	Het
Atp4b	A	C	8: 13,387,477	N225K	possibly damaging	Het
Auh	G	A	13: 52,835,496	P308L	probably benign	Het
Cactin	C	T	10: 81,322,893	T231I	possibly damaging	Het
Casp8ap2	T	C	4: 32,644,560	V1211A	probably benign	Het
Ccdc180	C	A	4: 45,944,418	H1423N	probably benign	Het
Chd9	T	C	8: 91,035,054	Y2256H	probably benign	Het
Chst8	A	G	7: 34,675,164	Y417H	possibly damaging	Het
Clcn6	A	G	4: 148,010,652		probably null	Het
Clec5a	A	T	6: 40,585,194	V12E	probably damaging	Het
Crebbp	C	T	16: 4,085,819	R1852H	probably damaging	Het
Cyp2c40	T	A	19: 39,812,780		probably benign	Het
Dip2c	T	C	13: 9,551,800	L265P	probably damaging	Het
Dnah3	A	G	7: 119,951,242	Y3274H	probably damaging	Het
Dnah6	T	A	6: 73,027,422	T3853S	probably benign	Het
Dnttip2	T	C	3: 122,276,221	S362P	probably damaging	Het
Dst	G	A	1: 34,166,291	V1025I	possibly damaging	Het
Dym	T	C	18: 75,080,250	V181A	probably benign	Het
Elk3	T	A	10: 93,265,677	I71F	probably damaging	Het
Epb41l4a	C	T	18: 33,921,840	S65N	probably benign	Het
Erap1	T	A	13: 74,666,508	V451E	probably benign	Het
F830045P16Rik	T	A	2: 129,472,665	I231F	probably damaging	Het
Fahd1	T	C	17: 24,849,840	I88V	probably benign	Het
Fam120b	C	T	17: 15,424,376	T744I	possibly damaging	Het
Fam83f	T	G	15: 80,692,267	V373G	possibly damaging	Het
Gdap1l1	A	T	2: 163,447,597	T161S	probably benign	Het
Gm5346	A	T	8: 43,625,917	C423*	probably null	Het
Gm597	A	T	1: 28,778,153	V266D	probably damaging	Het
Gm6309	C	T	5: 146,168,311	G264D	probably benign	Het
Gm9268	A	G	7: 43,024,030	N171D	probably benign	Het
Hsd11b1	T	C	1: 193,240,378	T124A	probably benign	Het
Ino80b	A	G	6: 83,124,372	M119T	probably damaging	Het
Kif3a	G	A	11: 53,570,581	V17M	probably damaging	Het
Krt40	T	A	11: 99,539,992	E285D	probably damaging	Het
Lair1	C	G	7: 4,063,064		probably null	Het
Lvrn	A	G	18: 46,866,436	T290A	possibly damaging	Het
Macf1	G	T	4: 123,472,730	A2746E	probably damaging	Het
Matn4	A	G	2: 164,400,653	V175A	probably damaging	Het
Mok	A	T	12: 110,811,823	D216E	probably benign	Het
Muc15	A	T	2: 110,731,476	T86S	probably benign	Het
Myo16	A	G	8: 10,272,633	K21R	probably benign	Het
Ncl	A	G	1: 86,356,955		probably null	Het
Nfrkb	C	T	9: 31,411,250	T872I	probably benign	Het
Nhlrc2	A	T	19: 56,597,278	E648D	probably benign	Het
Nlrp9c	A	T	7: 26,384,796	Y453N	probably damaging	Het
Notch4	T	C	17: 34,587,528	L1813P	probably damaging	Het
Nrg3	T	A	14: 38,376,352	D515V	probably damaging	Het
Nsd1	T	C	13: 55,213,279	V20A	probably damaging	Het
Olfr825	T	C	10: 130,163,180	M49V	probably benign	Het
Opn4	T	A	14: 34,597,071	T186S	probably benign	Het
Pcdh15	T	G	10: 74,631,193	S1684A	possibly damaging	Het
Phf11a	T	A	14: 59,294,914	E24V	possibly damaging	Het
Pigg	A	T	5: 108,312,922		probably benign	Het
Plscr2	A	G	9: 92,295,594	D136G	probably damaging	Het
Ppp3r2	T	C	4: 49,681,723	I76V	probably benign	Het
Prdm6	A	G	18: 53,464,959		probably benign	Het
Prex1	A	G	2: 166,575,614	W1188R	possibly damaging	Het
Prmt2	T	A	10: 76,225,458	R65*	probably null	Het
Prom1	G	T	5: 44,029,726	D396E	probably benign	Het
Ptcd3	C	T	6: 71,885,553	C466Y	probably damaging	Het
Ptk2	A	G	15: 73,242,406	V701A	possibly damaging	Het
Rab36	T	C	10: 75,052,474	I250T	probably benign	Het
Rsf1	G	A	7: 97,579,910		probably benign	Het
Scn11a	G	T	9: 119,811,208	A207E	possibly damaging	Het
Serpinb3d	A	G	1: 107,078,452	V302A	probably benign	Het
Slc22a16	T	C	10: 40,591,877	Y469H	probably damaging	Het
Smo	A	G	6: 29,754,716	N262D	possibly damaging	Het
Sptan1	C	T	2: 30,007,561	A1212V	probably damaging	Het
Ssr1	C	T	13: 37,989,549	A79T	probably damaging	Het
Tctex1d4	A	G	4: 117,128,307	E109G	possibly damaging	Het
Tiam1	T	A	16: 89,877,187	T479S	probably benign	Het
Tm9sf3	A	G	19: 41,238,792	F280S	probably damaging	Het
Tmem72	T	C	6: 116,696,839	H106R	probably damaging	Het
Tnr	A	G	1: 159,852,022	I189V	probably benign	Het
Tpbpa	T	A	13: 60,940,222	N50I	probably benign	Het
Tshz1	T	A	18: 84,013,862	Y807F	probably damaging	Het
Tspo2	C	T	17: 48,448,722	A131T	possibly damaging	Het
Usp16	T	C	16: 87,473,126	L322P	probably damaging	Het
Vmn1r185	A	G	7: 26,611,510	V190A	possibly damaging	Het
Vmn1r34	T	C	6: 66,637,401	K118E	possibly damaging	Het
Vmn1r68	A	G	7: 10,527,991	L60P	probably damaging	Het
Vps51	T	C	19: 6,071,582	E162G	probably benign	Het
Wdr66	G	A	5: 123,273,790	G495D	probably benign	Het
Yy1	CGGG	CGGGGGG	12: 108,793,990		probably benign	Het
Zdhhc4	C	T	5: 143,321,783	R161H	probably damaging	Het
Zfp456	A	T	13: 67,366,497	C363*	probably null	Het
Zfp541	T	A	7: 16,082,185	S866T	probably damaging	Het

Other mutations in Frem1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00155:Frem1	APN	4	82959389	missense	possibly damaging	0.46
IGL01069:Frem1	APN	4	83013867	missense	probably benign	0.00
IGL01106:Frem1	APN	4	82922257	missense	probably benign	0.00
IGL01398:Frem1	APN	4	82950362	missense	possibly damaging	0.64
IGL01617:Frem1	APN	4	82936139	missense	probably benign	0.02
IGL01647:Frem1	APN	4	82950356	missense	possibly damaging	0.60
IGL01690:Frem1	APN	4	82959296	splice site	probably benign
IGL02006:Frem1	APN	4	82992800	critical splice donor site	probably null
IGL02069:Frem1	APN	4	82903551	missense	probably damaging	1.00
IGL02131:Frem1	APN	4	82924854	missense	probably benign	0.03
IGL02225:Frem1	APN	4	82940506	missense	probably damaging	1.00
IGL02439:Frem1	APN	4	82956345	missense	probably benign	0.00
IGL02567:Frem1	APN	4	83000055	missense	probably damaging	1.00
IGL02647:Frem1	APN	4	83001754	missense	probably damaging	1.00
IGL02653:Frem1	APN	4	82959334	missense	probably benign	0.22
IGL02831:Frem1	APN	4	82956158	missense	probably benign	0.31
IGL02997:Frem1	APN	4	82934968	missense	probably damaging	1.00
IGL03005:Frem1	APN	4	82994134	missense	probably damaging	1.00
IGL03036:Frem1	APN	4	82959339	missense	possibly damaging	0.55
IGL03193:Frem1	APN	4	82994026	splice site	probably benign
IGL03218:Frem1	APN	4	82914646	missense	probably benign	0.00
IGL03235:Frem1	APN	4	83020755	missense	possibly damaging	0.87
IGL03243:Frem1	APN	4	83013969	missense	probably damaging	1.00
bat	UTSW	4	82983060	intron	probably benign
R4764_Frem1_085	UTSW	4	82989189	missense	probably damaging	1.00
PIT4131001:Frem1	UTSW	4	83005808	missense	probably damaging	0.99
PIT4466001:Frem1	UTSW	4	82972137	missense	probably benign	0.01
PIT4472001:Frem1	UTSW	4	82972137	missense	probably benign	0.01
PIT4515001:Frem1	UTSW	4	82900426	missense	probably damaging	0.98
PIT4531001:Frem1	UTSW	4	82950280	missense	probably benign	0.12
R0010:Frem1	UTSW	4	83000098	missense	probably benign	0.41
R0010:Frem1	UTSW	4	83000098	missense	probably benign	0.41
R0115:Frem1	UTSW	4	82936169	missense	possibly damaging	0.94
R0125:Frem1	UTSW	4	83011951	missense	probably damaging	1.00
R0280:Frem1	UTSW	4	82969444	missense	probably damaging	1.00
R0504:Frem1	UTSW	4	82912637	missense	probably benign	0.26
R0519:Frem1	UTSW	4	82970633	critical splice donor site	probably null
R0631:Frem1	UTSW	4	82972165	missense	probably damaging	1.00
R0645:Frem1	UTSW	4	82989166	missense	probably damaging	1.00
R0781:Frem1	UTSW	4	82950320	missense	probably damaging	0.99
R1110:Frem1	UTSW	4	82950320	missense	probably damaging	0.99
R1115:Frem1	UTSW	4	83020770	missense	probably benign	0.28
R1130:Frem1	UTSW	4	82916628	splice site	probably null
R1173:Frem1	UTSW	4	82950352	missense	probably benign	0.16
R1349:Frem1	UTSW	4	82922305	splice site	probably benign
R1464:Frem1	UTSW	4	83011879	missense	probably damaging	1.00
R1464:Frem1	UTSW	4	83011879	missense	probably damaging	1.00
R1658:Frem1	UTSW	4	83001808	missense	probably damaging	1.00
R1672:Frem1	UTSW	4	82998891	missense	probably benign	0.09
R1831:Frem1	UTSW	4	83020837	missense	possibly damaging	0.95
R1851:Frem1	UTSW	4	82950500	missense	probably damaging	0.98
R2014:Frem1	UTSW	4	83005852	missense	probably damaging	1.00
R2021:Frem1	UTSW	4	82913558	missense	probably benign	0.02
R2023:Frem1	UTSW	4	82913558	missense	probably benign	0.02
R2183:Frem1	UTSW	4	82991495	missense	probably benign	0.00
R2437:Frem1	UTSW	4	83000173	missense	probably damaging	1.00
R2520:Frem1	UTSW	4	82950290	missense	probably damaging	0.99
R3195:Frem1	UTSW	4	83014114	missense	probably damaging	0.99
R3196:Frem1	UTSW	4	83014114	missense	probably damaging	0.99
R3408:Frem1	UTSW	4	83011986	missense	probably damaging	1.00
R3411:Frem1	UTSW	4	82963179	missense	possibly damaging	0.51
R3742:Frem1	UTSW	4	83011867	missense	probably damaging	1.00
R3829:Frem1	UTSW	4	82998930	missense	probably damaging	1.00
R3888:Frem1	UTSW	4	82913607	missense	probably benign	0.41
R4329:Frem1	UTSW	4	82986537	missense	probably benign	0.01
R4364:Frem1	UTSW	4	82913251	missense	probably damaging	0.99
R4411:Frem1	UTSW	4	82963244	missense	probably damaging	1.00
R4624:Frem1	UTSW	4	82989106	missense	probably damaging	1.00
R4687:Frem1	UTSW	4	83020631	missense	probably damaging	1.00
R4764:Frem1	UTSW	4	82989189	missense	probably damaging	1.00
R4801:Frem1	UTSW	4	82916628	splice site	probably benign
R4802:Frem1	UTSW	4	82916628	splice site	probably benign
R4854:Frem1	UTSW	4	82916758	missense	possibly damaging	0.88
R4872:Frem1	UTSW	4	82963150	missense	probably damaging	1.00
R4947:Frem1	UTSW	4	82966134	missense	probably damaging	0.99
R5007:Frem1	UTSW	4	82940812	intron	probably benign
R5103:Frem1	UTSW	4	82991612	missense	probably benign
R5369:Frem1	UTSW	4	83001739	missense	possibly damaging	0.61
R5494:Frem1	UTSW	4	82940753	makesense	probably null
R5694:Frem1	UTSW	4	82994116	missense	probably damaging	1.00
R5780:Frem1	UTSW	4	82950415	missense	probably benign	0.12
R5813:Frem1	UTSW	4	83000158	missense	probably damaging	1.00
R5843:Frem1	UTSW	4	82936052	missense	probably damaging	1.00
R5914:Frem1	UTSW	4	83001775	missense	probably damaging	1.00
R5985:Frem1	UTSW	4	82966050	missense	probably benign
R6091:Frem1	UTSW	4	82900559	missense	probably benign	0.01
R6165:Frem1	UTSW	4	82956255	missense	probably benign	0.16
R6324:Frem1	UTSW	4	82983337	missense	probably benign	0.00
R6369:Frem1	UTSW	4	82913792	splice site	probably null
R6414:Frem1	UTSW	4	82940536	missense	probably damaging	0.98
R6421:Frem1	UTSW	4	82994128	missense	probably damaging	1.00
R6434:Frem1	UTSW	4	82966016	missense	probably benign	0.03
R6453:Frem1	UTSW	4	82914825	nonsense	probably null
R6598:Frem1	UTSW	4	83013828	missense	probably damaging	0.99
R6720:Frem1	UTSW	4	83013832	missense	probably damaging	0.98
R6862:Frem1	UTSW	4	83012014	nonsense	probably null
R6922:Frem1	UTSW	4	82922269	missense	probably damaging	1.00
R6931:Frem1	UTSW	4	82970677	missense	probably damaging	1.00
R6992:Frem1	UTSW	4	82940362	missense	possibly damaging	0.62
R6995:Frem1	UTSW	4	82986601	missense	probably damaging	1.00
R7001:Frem1	UTSW	4	82986561	missense	probably benign	0.44
R7104:Frem1	UTSW	4	82940681	missense	probably benign	0.30
R7146:Frem1	UTSW	4	82922295	missense	possibly damaging	0.93
R7174:Frem1	UTSW	4	82922256	missense	probably benign	0.00
R7327:Frem1	UTSW	4	83020755	missense	possibly damaging	0.87
R7343:Frem1	UTSW	4	82994122	missense	probably damaging	0.99
R7368:Frem1	UTSW	4	82966144	missense	probably benign	0.19
R7392:Frem1	UTSW	4	83013827	missense	probably benign	0.06
R7465:Frem1	UTSW	4	82914835	missense	probably benign	0.11
R7499:Frem1	UTSW	4	83005770	missense	probably damaging	1.00
R7536:Frem1	UTSW	4	82956195	missense	probably damaging	1.00
R7752:Frem1	UTSW	4	82959377	missense	probably benign	0.02
R7753:Frem1	UTSW	4	82913980	missense	probably benign	0.03
R7790:Frem1	UTSW	4	82989164	missense	probably benign	0.02
R7818:Frem1	UTSW	4	83014008	missense	probably damaging	1.00
R7877:Frem1	UTSW	4	83013812	critical splice donor site	probably null
R7878:Frem1	UTSW	4	83020680	missense	probably benign	0.00
R7886:Frem1	UTSW	4	83016406	missense	possibly damaging	0.68
R7901:Frem1	UTSW	4	82959377	missense	probably benign	0.02
R7976:Frem1	UTSW	4	83001709	missense	probably damaging	0.97
R8240:Frem1	UTSW	4	82956248	missense	probably benign	0.21
R8305:Frem1	UTSW	4	82999989	missense	probably benign	0.06
R8415:Frem1	UTSW	4	83000262	missense	probably damaging	1.00
R8751:Frem1	UTSW	4	82970778	missense	probably damaging	1.00
X0013:Frem1	UTSW	4	82914808	missense	probably benign	0.38
X0017:Frem1	UTSW	4	82991633	critical splice acceptor site	probably null
Z1088:Frem1	UTSW	4	82972267	missense	probably damaging	1.00
Z1176:Frem1	UTSW	4	82999983	missense	probably damaging	1.00
Z1177:Frem1	UTSW	4	82940315	critical splice donor site	probably null
Z1177:Frem1	UTSW	4	83000269	missense	probably benign	0.39
Z1177:Frem1	UTSW	4	83016464	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- AGCAGTTTCCTTCCTTGGG -3'
(R):5'- GCCTTGATGCTGTCTTTTAAATGC -3'

Sequencing Primer
(F):5'- GGGTCTTCATCTACAGTACAACATC -3'
(R):5'- AAAAGGTTTGTGTACTTTCTCAGTG -3'

Posted On

2014-08-25