Mutagenetix > Incidental Mutation

Incidental Mutation 'R7409:Slc52a3'

574897

Institutional Source

Beutler Lab

Gene Symbol

Slc52a3

Ensembl Gene

ENSMUSG00000027463

Gene Name

solute carrier protein family 52, member 3

Synonyms

2310046K01Rik

MMRRC Submission

045490-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R7409 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

151838431-151851178 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 151846086 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Serine to Proline at position 16 (S16P)

Ref Sequence

ENSEMBL: ENSMUSP00000072961 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000073228] [ENSMUST00000109858] [ENSMUST00000109859] [ENSMUST00000109861]

AlphaFold

Q9D6X5

Predicted Effect

probably damaging
Transcript: ENSMUST00000073228
AA Change: S16P

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000072961
Gene: ENSMUSG00000027463
AA Change: S16P

Domain	Start	End	E-Value	Type
transmembrane domain	7	29	N/A	INTRINSIC
transmembrane domain	39	61	N/A	INTRINSIC
transmembrane domain	74	96	N/A	INTRINSIC
transmembrane domain	106	128	N/A	INTRINSIC
transmembrane domain	141	163	N/A	INTRINSIC
transmembrane domain	210	232	N/A	INTRINSIC
Pfam:DUF1011	285	386	7.6e-47	PFAM
transmembrane domain	390	412	N/A	INTRINSIC
transmembrane domain	419	441	N/A	INTRINSIC

Predicted Effect

probably damaging
Transcript: ENSMUST00000109858
AA Change: S16P

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000105484
Gene: ENSMUSG00000027463
AA Change: S16P

Domain	Start	End	E-Value	Type
transmembrane domain	7	29	N/A	INTRINSIC
transmembrane domain	39	61	N/A	INTRINSIC
transmembrane domain	74	96	N/A	INTRINSIC
transmembrane domain	106	128	N/A	INTRINSIC
transmembrane domain	135	157	N/A	INTRINSIC

Predicted Effect

probably damaging
Transcript: ENSMUST00000109859
AA Change: S16P

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000105485
Gene: ENSMUSG00000027463
AA Change: S16P

Domain	Start	End	E-Value	Type
transmembrane domain	7	29	N/A	INTRINSIC
transmembrane domain	39	61	N/A	INTRINSIC
transmembrane domain	74	96	N/A	INTRINSIC
transmembrane domain	106	128	N/A	INTRINSIC
transmembrane domain	135	157	N/A	INTRINSIC

Predicted Effect

probably damaging
Transcript: ENSMUST00000109861
AA Change: S16P

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000105487
Gene: ENSMUSG00000027463
AA Change: S16P

Domain	Start	End	E-Value	Type
transmembrane domain	7	29	N/A	INTRINSIC
transmembrane domain	39	61	N/A	INTRINSIC
transmembrane domain	74	96	N/A	INTRINSIC
transmembrane domain	106	128	N/A	INTRINSIC
transmembrane domain	141	163	N/A	INTRINSIC
transmembrane domain	210	232	N/A	INTRINSIC
Pfam:DUF1011	288	386	1.1e-42	PFAM
transmembrane domain	390	412	N/A	INTRINSIC
transmembrane domain	419	441	N/A	INTRINSIC

Meta Mutation Damage Score

0.9371

Coding Region Coverage

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

Validation Efficiency

98% (82/84)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a riboflavin transporter protein that is strongly expressed in the intestine and likely plays a role in intestinal absorption of riboflavin. The protein is predicted to have eleven transmembrane domains and a cell surface localization signal in the C-terminus. Mutations at this locus have been associated with Brown-Vialetto-Van Laere syndrome and Fazio-Londe disease. [provided by RefSeq, Mar 2012]
PHENOTYPE: Mice homozygous for a knock-out allele exhibit abnormal placental riboflavin transport and sudden neonatal death associated with hyperlipidemia and hypoglycemia due to riboflavin deficiency. [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
Adgrb2	C	T	4: 129,912,862 (GRCm39)	A1329V	probably benign	Het
Aida	A	G	1: 183,099,809 (GRCm39)	T215A	probably benign	Het
Alpk2	A	G	18: 65,440,023 (GRCm39)	S457P	probably benign	Het
Ap4b1	G	A	3: 103,719,474 (GRCm39)	V63I	probably damaging	Het
Apaf1	A	G	10: 90,903,108 (GRCm39)	V182A	probably damaging	Het
B4galnt4	G	A	7: 140,646,916 (GRCm39)		probably null	Het
Bltp2	G	T	11: 78,159,583 (GRCm39)	R544L	probably damaging	Het
Cacna1a	T	G	8: 85,260,031 (GRCm39)	D331E	probably damaging	Het
Carmil2	A	G	8: 106,419,423 (GRCm39)		probably null	Het
Cdkn1b	A	T	6: 134,898,280 (GRCm39)	Q133L	probably benign	Het
Cep192	G	C	18: 67,967,874 (GRCm39)	S786T	possibly damaging	Het
Cfap418	T	A	4: 10,881,834 (GRCm39)	C94S	probably benign	Het
Cfap97	G	A	8: 46,645,733 (GRCm39)	R537H	probably benign	Het
Clpx	C	G	9: 65,231,529 (GRCm39)	A552G	possibly damaging	Het
Cryl1	G	A	14: 57,523,842 (GRCm39)	T240I	probably damaging	Het
Ddx60	C	A	8: 62,411,612 (GRCm39)	T488K	probably benign	Het
Dennd4b	A	G	3: 90,181,259 (GRCm39)	H805R	probably benign	Het
Dnmbp	T	C	19: 43,878,996 (GRCm39)	D25G	unknown	Het
Dysf	A	C	6: 84,126,664 (GRCm39)	D1293A	probably benign	Het
Efl1	T	C	7: 82,347,121 (GRCm39)	L549P	probably damaging	Het
Eif5	T	C	12: 111,506,697 (GRCm39)		probably benign	Het
Eva1c	A	G	16: 90,666,544 (GRCm39)	K156E	probably damaging	Het
Fbxw10	T	G	11: 62,767,606 (GRCm39)	V814G	possibly damaging	Het
Gfap	C	T	11: 102,785,358 (GRCm39)	R206Q	probably benign	Het
Gjb6	A	T	14: 57,361,610 (GRCm39)	L217*	probably null	Het
Gpatch11	T	A	17: 79,146,595 (GRCm39)	L80Q	probably damaging	Het
Gramd1b	T	C	9: 40,238,727 (GRCm39)	Q225R	probably damaging	Het
Gsdmc2	A	G	15: 63,705,195 (GRCm39)	S173P	possibly damaging	Het
Hars1	C	G	18: 36,903,166 (GRCm39)	R388P	probably damaging	Het
Ighm	C	T	12: 113,385,852 (GRCm39)	R129H		Het
Igsf9	A	G	1: 172,322,841 (GRCm39)	I602V	probably benign	Het
Inpp4b	T	G	8: 82,679,314 (GRCm39)		probably null	Het
Itch	C	A	2: 155,041,302 (GRCm39)	T450K	probably damaging	Het
Kcnq1	T	C	7: 142,663,152 (GRCm39)	F20L	unknown	Het
Kmt2d	G	T	15: 98,753,235 (GRCm39)	A153E	probably damaging	Het
Macf1	T	A	4: 123,398,263 (GRCm39)	N750I	probably damaging	Het
Marveld2	T	A	13: 100,747,984 (GRCm39)	H365L	probably damaging	Het
Med13l	T	A	5: 118,892,386 (GRCm39)	D1936E	probably benign	Het
Mettl8	A	T	2: 70,803,687 (GRCm39)	V200E	probably damaging	Het
Mrgbp	T	G	2: 180,227,135 (GRCm39)	S157A	possibly damaging	Het
Mrps35	A	G	6: 146,957,481 (GRCm39)	T169A	possibly damaging	Het
Mycbp2	A	T	14: 103,526,180 (GRCm39)	Y551N	probably damaging	Het
Myo18b	T	C	5: 113,021,971 (GRCm39)	R474G	probably benign	Het
Nfx1	T	A	4: 41,021,830 (GRCm39)	S979R	possibly damaging	Het
Nlrp1a	T	C	11: 71,013,634 (GRCm39)	T539A	probably benign	Het
Oca2	T	A	7: 56,064,145 (GRCm39)	D713E	probably benign	Het
Omt2b	A	C	9: 78,235,894 (GRCm39)	Y73S	probably benign	Het
Or10aa1	T	A	1: 173,870,099 (GRCm39)	H194Q	probably benign	Het
Or13a27	C	T	7: 139,925,318 (GRCm39)	V195I	probably benign	Het
Or6c38	A	G	10: 128,929,081 (GRCm39)	I254T	probably damaging	Het
Or6c69	A	T	10: 129,748,120 (GRCm39)	V9D	possibly damaging	Het
Pde11a	G	T	2: 75,836,328 (GRCm39)	Q20K		Het
Peg10	CCACATCAGGATCCACATCAGGATGCACATCAGCATCAGGATCCCCATCAGGATGCACATCAGGATCCACATCAGGATGCACATCAG	CCACATCAGGATCCACATCAGGATGCACATCAG	6: 4,756,398 (GRCm39)		probably benign	Het
Phrf1	C	A	7: 140,839,205 (GRCm39)	T800K	unknown	Het
Polr1f	T	G	12: 33,486,988 (GRCm39)	C150W	possibly damaging	Het
Pramel4	T	C	4: 143,795,061 (GRCm39)	S486P	probably benign	Het
Proc	T	C	18: 32,260,513 (GRCm39)	D204G	probably benign	Het
Rasgrp3	T	A	17: 75,823,411 (GRCm39)	I494N	possibly damaging	Het
Samm50	A	G	15: 84,081,231 (GRCm39)	D53G	probably benign	Het
Satb1	T	C	17: 52,116,217 (GRCm39)	D22G	possibly damaging	Het
Scarf2	T	C	16: 17,624,918 (GRCm39)	S658P	probably damaging	Het
Sfta2	T	A	17: 35,925,410 (GRCm39)	I29K	unknown	Het
Slc15a4	A	T	5: 127,681,742 (GRCm39)	S292T	probably benign	Het
Slc37a1	C	T	17: 31,559,237 (GRCm39)	T439I	probably damaging	Het
Slc4a9	C	A	18: 36,663,858 (GRCm39)	P294Q	probably damaging	Het
Slc6a15	A	G	10: 103,244,163 (GRCm39)	I468V	probably benign	Het
Spag17	T	C	3: 99,934,547 (GRCm39)	S610P	possibly damaging	Het
Spag17	A	T	3: 99,941,475 (GRCm39)	D738V	probably benign	Het
Ssbp4	T	C	8: 71,050,617 (GRCm39)	R269G	unknown	Het
Tbl1xr1	A	G	3: 22,257,354 (GRCm39)	T406A	possibly damaging	Het
Tep1	A	T	14: 51,104,312 (GRCm39)	V194D	possibly damaging	Het
Thbs4	A	T	13: 92,909,767 (GRCm39)	C343*	probably null	Het
Tmed10	A	T	12: 85,391,065 (GRCm39)	S158T	possibly damaging	Het
Trbv3	T	A	6: 41,025,524 (GRCm39)	V38E	probably damaging	Het
Ttc6	T	C	12: 57,743,772 (GRCm39)	M1258T	probably damaging	Het
Ttn	T	C	2: 76,589,320 (GRCm39)	D21281G	probably damaging	Het
Usp54	T	C	14: 20,602,313 (GRCm39)	R1346G	probably damaging	Het
Vmn2r8	C	A	5: 108,956,449 (GRCm39)	E58*	probably null	Het
Vps13d	C	T	4: 144,867,824 (GRCm39)	E2009K		Het
Vps33b	T	C	7: 79,935,017 (GRCm39)	I320T	probably damaging	Het
Vwa8	A	C	14: 79,219,674 (GRCm39)		probably null	Het
Ythdf1	T	C	2: 180,553,786 (GRCm39)	Y143C	probably damaging	Het
Zfp213	C	T	17: 23,778,603 (GRCm39)		probably null	Het
Zfp219	A	T	14: 52,244,570 (GRCm39)	Y536*	probably null	Het

Other mutations in Slc52a3

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01391:Slc52a3	APN	2	151,849,522 (GRCm39)	missense	probably benign	0.41
IGL01511:Slc52a3	APN	2	151,846,564 (GRCm39)	missense	probably benign	0.00
IGL02058:Slc52a3	APN	2	151,847,811 (GRCm39)	missense	probably damaging	1.00
IGL02271:Slc52a3	APN	2	151,847,448 (GRCm39)	splice site	probably benign
R0238:Slc52a3	UTSW	2	151,850,076 (GRCm39)	makesense	probably null
R0238:Slc52a3	UTSW	2	151,850,076 (GRCm39)	makesense	probably null
R0239:Slc52a3	UTSW	2	151,850,076 (GRCm39)	makesense	probably null
R0239:Slc52a3	UTSW	2	151,850,076 (GRCm39)	makesense	probably null
R0352:Slc52a3	UTSW	2	151,849,433 (GRCm39)	nonsense	probably null
R3727:Slc52a3	UTSW	2	151,847,701 (GRCm39)	missense	probably benign	0.00
R4272:Slc52a3	UTSW	2	151,847,660 (GRCm39)	missense	possibly damaging	0.87
R4273:Slc52a3	UTSW	2	151,847,660 (GRCm39)	missense	possibly damaging	0.87
R6267:Slc52a3	UTSW	2	151,849,529 (GRCm39)	splice site	probably null
R7265:Slc52a3	UTSW	2	151,846,336 (GRCm39)	missense	possibly damaging	0.78
R7634:Slc52a3	UTSW	2	151,846,534 (GRCm39)	missense	possibly damaging	0.49
R8697:Slc52a3	UTSW	2	151,846,396 (GRCm39)	missense	probably damaging	1.00
R8822:Slc52a3	UTSW	2	151,846,513 (GRCm39)	missense	probably benign
R9243:Slc52a3	UTSW	2	151,846,512 (GRCm39)	missense	probably benign
R9443:Slc52a3	UTSW	2	151,846,299 (GRCm39)	missense	probably benign

Predicted Primers

PCR Primer
(F):5'- CAGTTGTTGGTTTGCAACAACTC -3'
(R):5'- GAAGATCACAGGCACCTCAG -3'

Sequencing Primer
(F):5'- GCCCAGTTAAAGGTTATCTGTGAAC -3'
(R):5'- CCTCAGACAGGCAGCCG -3'

Posted On

2019-10-07