Mutagenetix > Incidental Mutation

Incidental Mutation 'R7272:Sdc1'

565365

Institutional Source

Beutler Lab

Gene Symbol

Sdc1

Ensembl Gene

ENSMUSG00000020592

Gene Name

syndecan 1

Synonyms

CD138, syn-1, Synd, Synd1

MMRRC Submission

045391-MU

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.230) question?

Stock #

R7272 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

8821396-8843716 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 8840554 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Histidine to Glutamine at position 106 (H106Q)

Ref Sequence

ENSEMBL: ENSMUSP00000020911 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000020911] [ENSMUST00000161883] [ENSMUST00000171158]

AlphaFold

P18828

Predicted Effect

probably benign
Transcript: ENSMUST00000020911
AA Change: H106Q

PolyPhen 2 Score 0.412 (Sensitivity: 0.89; Specificity: 0.90)

SMART Domains

Protein: ENSMUSP00000020911
Gene: ENSMUSG00000020592
AA Change: H106Q

Domain	Start	End	E-Value	Type
signal peptide	1	22	N/A	INTRINSIC
low complexity region	33	50	N/A	INTRINSIC
low complexity region	71	86	N/A	INTRINSIC
low complexity region	137	152	N/A	INTRINSIC
low complexity region	253	266	N/A	INTRINSIC
4.1m	276	294	5.47e-6	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000161883
AA Change: H110Q

PolyPhen 2 Score 0.230 (Sensitivity: 0.91; Specificity: 0.88)

SMART Domains

Protein: ENSMUSP00000123896
Gene: ENSMUSG00000020592
AA Change: H110Q

Domain	Start	End	E-Value	Type
low complexity region	37	54	N/A	INTRINSIC
low complexity region	75	90	N/A	INTRINSIC
low complexity region	141	156	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000171158
AA Change: H106Q

PolyPhen 2 Score 0.412 (Sensitivity: 0.89; Specificity: 0.90)

SMART Domains

Protein: ENSMUSP00000131491
Gene: ENSMUSG00000020592
AA Change: H106Q

Domain	Start	End	E-Value	Type
signal peptide	1	22	N/A	INTRINSIC
low complexity region	33	50	N/A	INTRINSIC
low complexity region	71	86	N/A	INTRINSIC
low complexity region	137	152	N/A	INTRINSIC
low complexity region	253	266	N/A	INTRINSIC
4.1m	276	294	5.47e-6	SMART

Meta Mutation Damage Score

0.0898

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.7%
20x: 98.9%

Validation Efficiency

100% (55/55)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The protein encoded by this gene is a transmembrane (type I) heparan sulfate proteoglycan and is a member of the syndecan proteoglycan family. The syndecans mediate cell binding, cell signaling, and cytoskeletal organization and syndecan receptors are required for internalization of the HIV-1 tat protein. The syndecan-1 protein functions as an integral membrane protein and participates in cell proliferation, cell migration and cell-matrix interactions via its receptor for extracellular matrix proteins. Altered syndecan-1 expression has been detected in several different tumor types. While several transcript variants may exist for this gene, the full-length natures of only two have been described to date. These two represent the major variants of this gene and encode the same protein. [provided by RefSeq, Jul 2008]
PHENOTYPE: Targeted mutant mice are overtly normal but resist mammary tumor development in response to Wnt1, and show delayed cutaneous and corneal wound healing, defective leukocyte adhesion to endothelia, increased angiogenesis, as well as reduced susceptibility to P. aeruginosa lung infection. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 54 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
2210408I21Rik	T	C	13: 77,471,655 (GRCm39)	I1020T	probably benign	Het
2310057N15Rik	A	T	16: 88,570,523 (GRCm39)	Y172*	probably null	Het
4930558K02Rik	T	A	1: 161,770,092 (GRCm39)	Y139F	possibly damaging	Het
A830018L16Rik	T	G	1: 11,658,695 (GRCm39)	M202R	probably damaging	Het
Abca12	T	C	1: 71,287,591 (GRCm39)	E2450G	probably damaging	Het
Ank2	C	T	3: 126,736,782 (GRCm39)	R3034H	unknown	Het
Anxa9	A	G	3: 95,213,184 (GRCm39)	I54T	probably damaging	Het
Ash1l	A	G	3: 88,961,941 (GRCm39)		probably null	Het
Aspm	T	C	1: 139,386,066 (GRCm39)	I570T	probably benign	Het
Bcar3	A	T	3: 122,302,045 (GRCm39)	I247F	possibly damaging	Het
Cep350	A	G	1: 155,829,334 (GRCm39)	V130A	probably damaging	Het
Cep89	A	T	7: 35,137,888 (GRCm39)	R757S	probably benign	Het
Cryga	A	T	1: 65,142,381 (GRCm39)	I4N	probably damaging	Het
Cyp2d26	T	A	15: 82,676,764 (GRCm39)	Y194F	probably benign	Het
Edn2	G	A	4: 120,019,143 (GRCm39)	R44H	probably damaging	Het
Ep400	G	A	5: 110,903,511 (GRCm39)	Q363*	probably null	Het
Gpr33	T	C	12: 52,070,848 (GRCm39)	T64A	probably damaging	Het
Ice2	T	A	9: 69,324,365 (GRCm39)	S763T	possibly damaging	Het
Itgad	C	A	7: 127,804,245 (GRCm39)	F1169L	probably damaging	Het
Kcnv1	A	G	15: 44,976,576 (GRCm39)	L237P	probably benign	Het
Kctd18	T	C	1: 57,995,710 (GRCm39)	E356G	probably damaging	Het
Krt33a	C	T	11: 99,902,837 (GRCm39)	R329Q	probably damaging	Het
Lama2	C	A	10: 27,000,552 (GRCm39)	G1657C	probably damaging	Het
Marchf3	T	G	18: 56,895,593 (GRCm39)	R217S	probably benign	Het
Mmel1	A	T	4: 154,978,547 (GRCm39)	T660S	probably damaging	Het
Ms4a7	T	A	19: 11,310,642 (GRCm39)	K59*	probably null	Het
Mss51	G	A	14: 20,534,981 (GRCm39)	T263I	probably damaging	Het
Ncaph2	A	G	15: 89,248,385 (GRCm39)	M199V	probably benign	Het
Ndufa4	G	A	6: 11,905,209 (GRCm39)	Q62*	probably null	Het
Nectin4	A	G	1: 171,214,212 (GRCm39)	T456A	probably damaging	Het
Nek1	T	C	8: 61,578,120 (GRCm39)	M1214T	probably benign	Het
Nsf	T	A	11: 103,718,064 (GRCm39)	L710F	probably damaging	Het
Nynrin	G	T	14: 56,107,872 (GRCm39)	G993V	probably damaging	Het
Or1e31	T	A	11: 73,689,695 (GRCm39)	D296V	probably damaging	Het
Pbk	T	A	14: 66,052,621 (GRCm39)	Y155N	probably damaging	Het
Plec	T	C	15: 76,059,153 (GRCm39)	I3595V	possibly damaging	Het
Pom121	G	A	5: 135,409,941 (GRCm39)	T1072I	unknown	Het
Slc44a3	T	C	3: 121,254,764 (GRCm39)	D618G	probably damaging	Het
Slc9c1	A	G	16: 45,401,878 (GRCm39)	D755G	possibly damaging	Het
Slfn9	T	C	11: 82,872,387 (GRCm39)	Y783C	probably benign	Het
Sorl1	C	T	9: 41,975,006 (GRCm39)		probably null	Het
Spindoc	C	T	19: 7,360,085 (GRCm39)	E28K	possibly damaging	Het
Sptbn1	T	C	11: 30,064,859 (GRCm39)	D1880G	possibly damaging	Het
Sspn	T	A	6: 145,907,200 (GRCm39)	D210E	probably benign	Het
Stx12	A	T	4: 132,584,687 (GRCm39)	I219K	possibly damaging	Het
Syne2	T	C	12: 76,095,417 (GRCm39)	V508A	probably benign	Het
Tkt	G	T	14: 30,287,564 (GRCm39)	R186L	probably damaging	Het
Trmt10a	T	A	3: 137,860,527 (GRCm39)	M241K	probably damaging	Het
Vgll2	C	A	10: 51,903,758 (GRCm39)	A207E	possibly damaging	Het
Vmn1r114	A	G	7: 20,545,543 (GRCm39)	F190S	probably damaging	Het
Xpot	C	T	10: 121,453,094 (GRCm39)		probably null	Het
Yrdc	G	A	4: 124,744,820 (GRCm39)	A85T	probably benign	Het
Zfp385c	C	T	11: 100,520,865 (GRCm39)	R265K	possibly damaging	Het
Zgrf1	A	T	3: 127,392,409 (GRCm39)	I1310F	probably damaging	Het

Other mutations in Sdc1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00090:Sdc1	APN	12	8,840,459 (GRCm39)	missense	possibly damaging	0.75
IGL02197:Sdc1	APN	12	8,840,835 (GRCm39)	missense	possibly damaging	0.90
E0374:Sdc1	UTSW	12	8,839,424 (GRCm39)	missense	probably damaging	1.00
R1673:Sdc1	UTSW	12	8,840,409 (GRCm39)	missense	possibly damaging	0.66
R4700:Sdc1	UTSW	12	8,840,541 (GRCm39)	missense	possibly damaging	0.82
R4887:Sdc1	UTSW	12	8,841,708 (GRCm39)	missense	probably damaging	1.00
R5396:Sdc1	UTSW	12	8,841,743 (GRCm39)	splice site	probably null
R6358:Sdc1	UTSW	12	8,841,297 (GRCm39)	missense	probably damaging	0.99
R7575:Sdc1	UTSW	12	8,840,619 (GRCm39)	missense	probably damaging	1.00
R7741:Sdc1	UTSW	12	8,841,370 (GRCm39)	missense	probably benign	0.06
R8125:Sdc1	UTSW	12	8,840,663 (GRCm39)	missense	probably benign	0.01
R8900:Sdc1	UTSW	12	8,840,460 (GRCm39)	missense	possibly damaging	0.92
R9096:Sdc1	UTSW	12	8,841,665 (GRCm39)	missense	probably damaging	1.00
R9225:Sdc1	UTSW	12	8,821,817 (GRCm39)	missense	unknown

Predicted Primers

PCR Primer
(F):5'- AGGTGCTTTGCCAGATACTTTG -3'
(R):5'- TTTGATGACAGAAGTGCCGCC -3'

Sequencing Primer
(F):5'- CCAGATACTTTGTCACGGCAG -3'
(R):5'- ACACGTGGAGGCTGATGGTC -3'

Posted On

2019-06-26