Mutagenetix > Incidental Mutation

Incidental Mutation 'R8815:Sdc3'

672655

Institutional Source

Beutler Lab

Gene Symbol

Sdc3

Ensembl Gene

ENSMUSG00000025743

Gene Name

syndecan 3

Synonyms

syn-3, Synd3

MMRRC Submission

068650-MU

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.117) question?

Stock #

R8815 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

130519848-130553629 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 130546336 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Serine to Threonine at position 232 (S232T)

Ref Sequence

ENSEMBL: ENSMUSP00000065877 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000070478] [ENSMUST00000141297] [ENSMUST00000152591]

AlphaFold

Q64519

Predicted Effect

probably benign
Transcript: ENSMUST00000070478
AA Change: S232T

PolyPhen 2 Score 0.177 (Sensitivity: 0.92; Specificity: 0.87)

SMART Domains

Protein: ENSMUSP00000065877
Gene: ENSMUSG00000025743
AA Change: S232T

Domain	Start	End	E-Value	Type
signal peptide	1	44	N/A	INTRINSIC
low complexity region	60	76	N/A	INTRINSIC
low complexity region	101	115	N/A	INTRINSIC
low complexity region	123	154	N/A	INTRINSIC
low complexity region	157	202	N/A	INTRINSIC
low complexity region	213	240	N/A	INTRINSIC
low complexity region	276	287	N/A	INTRINSIC
low complexity region	330	341	N/A	INTRINSIC
4.1m	408	426	2.51e-5	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000141297
AA Change: S138T

PolyPhen 2 Score 0.177 (Sensitivity: 0.92; Specificity: 0.87)

SMART Domains

Protein: ENSMUSP00000123608
Gene: ENSMUSG00000025743
AA Change: S138T

Domain	Start	End	E-Value	Type
low complexity region	7	21	N/A	INTRINSIC
low complexity region	29	60	N/A	INTRINSIC
low complexity region	63	108	N/A	INTRINSIC
low complexity region	119	146	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000152591
AA Change: S138T

PolyPhen 2 Score 0.177 (Sensitivity: 0.92; Specificity: 0.87)

SMART Domains

Protein: ENSMUSP00000118685
Gene: ENSMUSG00000025743
AA Change: S138T

Domain	Start	End	E-Value	Type
low complexity region	7	21	N/A	INTRINSIC
low complexity region	29	60	N/A	INTRINSIC
low complexity region	63	108	N/A	INTRINSIC
low complexity region	119	146	N/A	INTRINSIC

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.8%
20x: 99.3%

Validation Efficiency

99% (70/71)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The protein encoded by this gene belongs to the syndecan proteoglycan family. It may play a role in the organization of cell shape by affecting the actin cytoskeleton, possibly by transferring signals from the cell surface in a sugar-dependent mechanism. Allelic variants of this gene have been associated with obesity. [provided by RefSeq, Oct 2009]
PHENOTYPE: Homozygotes for a targeted null mutation exhibit enhanced long-term potentiation and impaired hippocampus-dependent memory. [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
1700066M21Rik	A	T	1: 57,421,943 (GRCm39)	Q106H	probably damaging	Het
Acad9	T	C	3: 36,139,590 (GRCm39)	C397R	probably damaging	Het
Ankfn1	T	G	11: 89,282,602 (GRCm39)	R348S	probably damaging	Het
Ankrd61	A	G	5: 143,831,336 (GRCm39)	C28R	probably benign	Het
Ano5	C	T	7: 51,194,548 (GRCm39)	R94*	probably null	Het
Apela	A	T	8: 65,489,590 (GRCm39)	F10I	unknown	Het
Arhgap31	T	C	16: 38,429,790 (GRCm39)	S362G	probably benign	Het
Arhgef18	C	A	8: 3,430,410 (GRCm39)	H94Q	probably benign	Het
Astn2	A	T	4: 65,830,834 (GRCm39)	L585Q	possibly damaging	Het
Atf3	G	T	1: 190,909,564 (GRCm39)	A35D	probably benign	Het
Atp10b	A	T	11: 43,093,978 (GRCm39)	R507S	possibly damaging	Het
Brip1	A	C	11: 86,080,598 (GRCm39)	V156G	probably benign	Het
Ccdc27	T	A	4: 154,111,205 (GRCm39)	M636L	probably benign	Het
Ceacam5	T	A	7: 17,493,285 (GRCm39)	N769K	possibly damaging	Het
Cklf	C	T	8: 104,977,560 (GRCm39)		probably benign	Het
Cpeb4	G	A	11: 31,870,546 (GRCm39)	V474M	probably damaging	Het
Dip2c	T	A	13: 9,673,834 (GRCm39)	C1091*	probably null	Het
Eef1akmt4	T	A	16: 20,437,288 (GRCm39)	I210N	possibly damaging	Het
Fbxo38	A	T	18: 62,666,587 (GRCm39)	H195Q	probably damaging	Het
Fbxw14	G	A	9: 109,105,305 (GRCm39)	R287*	probably null	Het
Fes	A	G	7: 80,033,619 (GRCm39)	S211P	possibly damaging	Het
Fry	G	T	5: 150,317,603 (GRCm39)	R861L	possibly damaging	Het
Galnt12	A	G	4: 47,113,908 (GRCm39)		probably benign	Het
Gm14226	G	A	2: 154,866,538 (GRCm39)	W165*	probably null	Het
Gm40460	GCAGCAGCTGGACTGGCAGCAGCAGGGCTTACAGCAGCTGGACTGGCAGCAGCAGGGCTTACAGCAGCTGGACTGGCAGCAGCAGGGCTTACAGCAGCTGGACTGGCAGCAG	GCAGCAGCTGGACTGGCAGCAGCAGGGCTTACAGCAGCTGGACTGGCAGCAGCAGGGCTTACAGCAGCTGGACTGGCAGCAG	7: 141,794,171 (GRCm39)		probably benign	Het
Gm40460	CACAGCCTCCCTTGCAGCCCCCACAGGAACTACAGCCTCCCTTGCAGCCCCCACAGGAACTACAGCCTCCCTTGCAGCCCCCACAGGAACTACAGCCTCCCTTGCAGCCCCCACAG	CACAGCCTCCCTTGCAGCCCCCACAGGAACTACAGCCTCCCTTGCAGCCCCCACAGGAACTACAGCCTCCCTTGCAGCCCCCACAG	7: 141,794,554 (GRCm39)		probably benign	Het
Gprc6a	A	G	10: 51,497,079 (GRCm39)	V488A	probably benign	Het
Haus8	A	T	8: 71,705,910 (GRCm39)		probably benign	Het
Helb	A	T	10: 119,948,692 (GRCm39)	C26S	possibly damaging	Het
Icam1	A	T	9: 20,937,862 (GRCm39)	I300F	probably benign	Het
Ip6k1	A	G	9: 107,918,211 (GRCm39)	N181S	probably benign	Het
Itga2b	C	A	11: 102,351,687 (GRCm39)	R546L	possibly damaging	Het
Kif27	A	T	13: 58,476,818 (GRCm39)	Y611N	probably damaging	Het
Lpcat2	A	G	8: 93,640,979 (GRCm39)	I475V	possibly damaging	Het
Lrit2	A	G	14: 36,794,487 (GRCm39)	K517R	probably benign	Het
Lrp1b	A	T	2: 40,555,171 (GRCm39)	I4085N		Het
Lrrc32	T	A	7: 98,148,242 (GRCm39)	S341T	probably damaging	Het
Lrrn2	T	A	1: 132,866,831 (GRCm39)	I632K	possibly damaging	Het
Mettl22	A	G	16: 8,300,178 (GRCm39)	Q194R	probably benign	Het
Mfhas1	T	A	8: 36,057,394 (GRCm39)	V623E	probably damaging	Het
Mitd1	T	C	1: 37,929,315 (GRCm39)	D26G	probably damaging	Het
Myo1a	C	T	10: 127,546,043 (GRCm39)	T222M	probably benign	Het
Naf1	A	G	8: 67,317,333 (GRCm39)	K275R	possibly damaging	Het
Nf1	T	C	11: 79,332,491 (GRCm39)	L765P	probably damaging	Het
Or12k7	G	T	2: 36,958,429 (GRCm39)	M37I	probably benign	Het
Or52a5	A	G	7: 103,427,063 (GRCm39)	L163P	possibly damaging	Het
Or5ac16	T	A	16: 59,022,264 (GRCm39)	H175L	possibly damaging	Het
Or9r3	T	A	10: 129,947,808 (GRCm39)	I284F	probably damaging	Het
Pappa	A	G	4: 65,099,347 (GRCm39)	H622R	probably benign	Het
Pcdhb4	A	T	18: 37,442,055 (GRCm39)	Y455F	probably damaging	Het
Pepd	A	G	7: 34,671,116 (GRCm39)	Y220C	probably damaging	Het
Pias3	T	C	3: 96,607,381 (GRCm39)	I172T	probably damaging	Het
Polq	T	A	16: 36,853,893 (GRCm39)	H415Q	probably damaging	Het
Pp2d1	A	T	17: 53,814,897 (GRCm39)	M609K	probably benign	Het
Ppm1m	G	A	9: 106,076,237 (GRCm39)		probably benign	Het
Prss22	T	A	17: 24,215,662 (GRCm39)	T87S	probably benign	Het
Ptprf	C	A	4: 118,095,125 (GRCm39)	V254L	possibly damaging	Het
Ripply3	A	G	16: 94,136,723 (GRCm39)	E128G	possibly damaging	Het
Rrm2	A	C	12: 24,760,470 (GRCm39)	I185L	possibly damaging	Het
Sbsn	T	A	7: 30,454,227 (GRCm39)		probably benign	Het
Slx4	G	C	16: 3,803,458 (GRCm39)	P1119A	probably benign	Het
Smc5	C	T	19: 23,221,422 (GRCm39)	R369Q	probably damaging	Het
Speer4a3	A	G	5: 26,158,191 (GRCm39)	S54P	probably damaging	Het
Spns1	G	A	7: 125,971,593 (GRCm39)	S319F	possibly damaging	Het
Sptbn4	G	A	7: 27,106,657 (GRCm39)	Q924*	probably null	Het
Srcap	G	C	7: 127,158,037 (GRCm39)	D2638H	unknown	Het
Srsf12	T	C	4: 33,226,045 (GRCm39)	S103P	possibly damaging	Het
Tanc1	A	G	2: 59,621,185 (GRCm39)	T335A	possibly damaging	Het
Them4	C	T	3: 94,231,610 (GRCm39)	T149I	probably damaging	Het
Trpc7	T	C	13: 56,970,312 (GRCm39)	Y424C	possibly damaging	Het
Ttn	C	T	2: 76,628,364 (GRCm39)	D14599N	probably damaging	Het
Ttn	A	T	2: 76,698,244 (GRCm39)	L186H		Het
Usp17lc	T	C	7: 103,067,524 (GRCm39)	F273S	probably benign	Het
Vwa5b2	T	C	16: 20,419,516 (GRCm39)	S620P	probably damaging	Het

Other mutations in Sdc3

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00979:Sdc3	APN	4	130,545,991 (GRCm39)	missense	unknown
IGL01715:Sdc3	APN	4	130,546,378 (GRCm39)	missense	probably damaging	0.99
IGL02160:Sdc3	APN	4	130,545,886 (GRCm39)	splice site	probably benign
IGL03134:Sdc3	UTSW	4	130,548,815 (GRCm39)	missense	probably benign	0.00
R2426:Sdc3	UTSW	4	130,546,114 (GRCm39)	missense	unknown
R4678:Sdc3	UTSW	4	130,545,907 (GRCm39)	utr 5 prime	probably benign
R4779:Sdc3	UTSW	4	130,546,376 (GRCm39)	missense	probably damaging	0.99
R4786:Sdc3	UTSW	4	130,550,079 (GRCm39)	missense	probably damaging	0.97
R5182:Sdc3	UTSW	4	130,548,995 (GRCm39)	unclassified	probably benign
R5225:Sdc3	UTSW	4	130,546,087 (GRCm39)	missense	unknown
R6111:Sdc3	UTSW	4	130,546,153 (GRCm39)	missense	unknown
R6980:Sdc3	UTSW	4	130,544,233 (GRCm39)	utr 5 prime	probably benign
R7881:Sdc3	UTSW	4	130,544,244 (GRCm39)	missense	unknown
R7920:Sdc3	UTSW	4	130,546,507 (GRCm39)	missense	probably benign	0.00
R8514:Sdc3	UTSW	4	130,546,072 (GRCm39)	missense	unknown
R8909:Sdc3	UTSW	4	130,546,094 (GRCm39)	missense	unknown
R9116:Sdc3	UTSW	4	130,546,352 (GRCm39)	missense	probably benign	0.33
R9251:Sdc3	UTSW	4	130,548,513 (GRCm39)	unclassified	probably benign
R9764:Sdc3	UTSW	4	130,546,048 (GRCm39)	missense	unknown

Predicted Primers

PCR Primer
(F):5'- AACTATGGCCACAGCACCTG -3'
(R):5'- AACAGCCTTTACTCAGCTGGC -3'

Sequencing Primer
(F):5'- ACAGCACCTGCCACAGC -3'
(R):5'- TTACTCAGCTGGCCTGGC -3'

Posted On

2021-04-30