Reference SNP(refSNP) Cluster Report: rs28936690

Reference SNP(refSNP) Cluster Report: rs28936690

refSNP ID: rs28936690
Organism:	human (Homo sapiens)
Molecule Type:	cDNA
Created/Updated in build:	125/129
Map to Genome Build:	36.3

Allele
Variation Class:	SNP: single nucleotide polymorphism
RefSNP Alleles:	C/T
Ancestral Allele:	Not available
Clinical Association:	unknown

HGVS Names
NM_001089.2:c.4655T>C
NP_001080.2:p.L1552P
NT_037887.4:g.2268352A>G

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss38342198 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs28936690 during BLAST analysis for the current build.

NCBI Assay ID	Handle\|Submitter ID	Validation Status	ss to rs Orientation /Strand	Alleles	5' Near Seq 30 bp	3' Near Seq 30 bp	Entry Date	Update Date	Build Added	Molecule Type	Freq Warning	Ancestral Allele	Success Rate
ss38342198	OMIMSNP\|OMIM_601615_0003		fwd/B	C/T	ccactggcatggaccccgtggcccggcgcc	gctttgggacaccgtggcacgagcccgaga	05/17/05	05/17/05	125	cDNA			unknown

Fasta sequence (Legend)

 GACCACATGA CAGGCCGGGA GATGCTGGTC ATGTACGCTC GGCTCCGGGG CATCCCTGAG
 CGCCACATCG GGGCCTGCGT GGAGAACACT CTGCGGGGCC TGCTGCTGGA GCCACATGCC
 AACAAGCTGG TCAGGACGTA CAGTGGTGGT AACAAGCGGA AGCTGAGCAC CGGCATCGCC
 CTGATCGGAG AGCCTGCTGT CATCTTCCTG GACGAGCCGT CCACTGGCAT GGACCCCGTG
 GCCCGGCGCC
 Y
 GCTTTGGGAC ACCGTGGCAC GAGCCCGAGA GTCTGGCAAG GCCATCATCA TCACCTCCCA
 CAGCATGGAG GAGTGTGAGG CCCTGTGCAC CCGGCTGGCC ATCATGGTGC AGGGGCAGTT
 CAAGTGCCTG GGCAGCCCCC AGCACCTCAA GAGCAAGTTC GGCAGCGGCT ACTCCCTGCG
 GGCCAAGGTG CAGAGTGAAG GGCAACAGGA GGCGCTGGAG GAGTTCAAGG CCTTCGTGGA
 CCTGACCTTT

GeneView

GeneView via analysis of contig annotation: ABCA3 ATP-binding cassette, sub-family A (ABC1), member 3

View variations for gene:

Include clinically associated:

in gene region cSNP has frequency double hit

Group
Label

Contig->mRNA

Gene Model (contig mRNA transcript) Color Legend

reference

NT_037887->NM_001089

function

HuRef

NW_001838339->NM_001089

function

Celera

NW_926018->NM_001089

function

Group label	Contig-->mRNA-->Protein	Contig position	mRNA orientation	mRNA pos	Function	dbSNP allele	Protein residue	Codon pos	Amino acid pos


reference	NT_037887->NM_001089->NP_001080	2268353	reverse	5367	missense	C	Pro [P]	2	1552
					contig reference	T	Leu [L]	2	1552

HuRef	NW_001838339->NM_001089->NP_001080	369642	forward	5193	missense	C	Pro [P]	2	1552
					contig reference	T	Leu [L]	2	1552

Celera	NW_926018->NM_001089->NP_001080	2258431	reverse	5367	missense	C	Pro [P]	2	1552
					contig reference	T	Leu [L]	2	1552

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs28936690 maps exactly once on NCBI human chromosome 16

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
16	NW_001838339.2	369642	2254375	plus	T	alt_assembly_8	HuRef	HuRef	view	250
16	NT_037887.4	2268353	2268353	minus	A	ref_assembly	reference	reference	view	250
16	NW_926018.1	2258431	2542781	minus	A	alt_assembly_1	Celera	Celera	view	250

NCBI Resource Links

Submitter-Referenced
GenBank
1514529 1699037 19698201 4501848

dbSNP Blast Analysis
NCBI RefSeq NM (mRNA):	GenBank HTGS Finished:	GenBank HTGS Draft:	GenBank mRNA:
NM_001089.2	AC005212.1 AC007162.1 AC098805.2 NC_000016.8	AC012171.4	AB070929.1 AB210044.1 BC151840.1 U78735.1 X97187.1

OMIM
601615

Population Diversity

There is no frequency data.

Validation Summary:

Validation status	Marker displays Mendelian segregation	PCR results confirmed in multiple reactions	Homozygotes detected in individual genotype data
	UNKNOWN	UNKNOWN	UNKNOWN

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Revised: May 25, 2006 1:38 PM .