Name: rs142150953
Published: September 21, 2022
License: Open Access

Welcome to the Reference SNP (rs) Report

All alleles are reported in the Forward orientation. Click on the Variant Details tab for details on Genomic Placement, Gene, and Amino Acid changes. HGVS names are in the HGVS tab.

Reference SNP (rs) Report

This page reports data for a single dbSNP Reference SNP variation (RefSNP or rs) from the new redesigned dbSNP build.
Top of the page reports a concise summary for the rs, with more specific details included in the corresponding tabs below.
All alleles are reported in the Forward orientation. Use the Genomic View to inspect the nucleotides flanking the variant, and its neighbors.
For more information see Help documentation.

rs142150953

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr18:36213402 (GRCh38.p14) Help
The anchor position for this RefSNP. Includes all nucleotides potentially affected by this change, thus it can differ from HGVS, which is right-shifted. See here for details.
Alleles: C>A / C>T
Variation Type: SNV Single Nucleotide Variation
Frequency: T=0.000263 (66/251260, GnomAD_exome)
T=0.000252 (48/190294, ALFA)
T=0.000107 (15/140238, GnomAD) (+ 8 more)
T=0.000239 (29/121154, ExAC)
T=0.00005 (4/78702, PAGE_STUDY)
T=0.00007 (2/28258, 14KJPN)
T=0.00006 (1/16760, 8.3KJPN)
T=0.00031 (4/13006, GO-ESP)
T=0.0002 (1/5008, 1000G)
T=0.0003 (1/3854, ALSPAC)
T=0.0003 (1/3708, TWINSUK)

Clinical Significance: Reported in ClinVar
Gene : Consequence: MOCOS : Stop Gained
Publications: 2 citations
Genomic View: See rs on genome

ALFA Allele Frequency
The ALFA project provide aggregate allele frequency from dbGaP. More information is available on the project page including descriptions, data access, and terms of use.

Release Version: 20230706150541

Population	Group	Sample Size	Ref Allele	Alt Allele
Total	Global	206700	C=0.999753	A=0.000000, T=0.000247
European	Sub	174012	C=0.999736	A=0.000000, T=0.000264
African	Sub	9198	C=1.0000	A=0.0000, T=0.0000
African Others	Sub	352	C=1.000	A=0.000, T=0.000
African American	Sub	8846	C=1.0000	A=0.0000, T=0.0000
Asian	Sub	6294	C=0.9998	A=0.0000, T=0.0002
East Asian	Sub	4476	C=1.0000	A=0.0000, T=0.0000
Other Asian	Sub	1818	C=0.9994	A=0.0000, T=0.0006
Latin American 1	Sub	796	C=1.000	A=0.000, T=0.000
Latin American 2	Sub	968	C=1.000	A=0.000, T=0.000
South Asian	Sub	280	C=1.000	A=0.000, T=0.000
Other	Sub	15152	C=0.99974	A=0.00000, T=0.00026

Frequency tab displays a table of the reference and alternate allele frequencies reported by various studies and populations. Table lines, where Population="Global" refer to the entire study population, whereas lines, where Group="Sub", refer to a study-specific population subgroupings (i.e. AFR, CAU, etc.), if available. Frequency for the alternate allele (Alt Allele) is a ratio of samples observed-to-total, where the numerator (observed samples) is the number of chromosomes in the study with the minor allele present (found in "Sample size", where Group="Sub"), and the denominator (total samples) is the total number of all chromosomes in the study for the variant (found in "Sample size", where Group="Study-wide" and Population="Global").

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Study	Population	Group	Sample Size	Ref Allele	Alt Allele
gnomAD - Exomes	Global	Study-wide	251260	C=0.999737	T=0.000263
gnomAD - Exomes	European	Sub	135238	C=0.999704	T=0.000296
gnomAD - Exomes	Asian	Sub	48990	C=0.99967	T=0.00033
gnomAD - Exomes	American	Sub	34572	C=0.99971	T=0.00029
gnomAD - Exomes	African	Sub	16254	C=1.00000	T=0.00000
gnomAD - Exomes	Ashkenazi Jewish	Sub	10074	C=1.00000	T=0.00000
gnomAD - Exomes	Other	Sub	6132	C=1.0000	T=0.0000
Allele Frequency Aggregator	Total	Global	190294	C=0.999748	A=0.000000, T=0.000252
Allele Frequency Aggregator	European	Sub	163878	C=0.999738	A=0.000000, T=0.000262
Allele Frequency Aggregator	Other	Sub	13718	C=0.99971	A=0.00000, T=0.00029
Allele Frequency Aggregator	Asian	Sub	6294	C=0.9998	A=0.0000, T=0.0002
Allele Frequency Aggregator	African	Sub	4360	C=1.0000	A=0.0000, T=0.0000
Allele Frequency Aggregator	Latin American 2	Sub	968	C=1.000	A=0.000, T=0.000
Allele Frequency Aggregator	Latin American 1	Sub	796	C=1.000	A=0.000, T=0.000
Allele Frequency Aggregator	South Asian	Sub	280	C=1.000	A=0.000, T=0.000
gnomAD - Genomes	Global	Study-wide	140238	C=0.999893	T=0.000107
gnomAD - Genomes	European	Sub	75932	C=0.99986	T=0.00014
gnomAD - Genomes	African	Sub	42034	C=0.99995	T=0.00005
gnomAD - Genomes	American	Sub	13662	C=0.99993	T=0.00007
gnomAD - Genomes	Ashkenazi Jewish	Sub	3322	C=1.0000	T=0.0000
gnomAD - Genomes	East Asian	Sub	3134	C=1.0000	T=0.0000
gnomAD - Genomes	Other	Sub	2154	C=0.9995	T=0.0005
ExAC	Global	Study-wide	121154	C=0.999761	T=0.000239
ExAC	Europe	Sub	73246	C=0.99973	T=0.00027
ExAC	Asian	Sub	25080	C=0.99976	T=0.00024
ExAC	American	Sub	11536	C=0.99974	T=0.00026
ExAC	African	Sub	10390	C=1.00000	T=0.00000
ExAC	Other	Sub	902	C=1.000	T=0.000
The PAGE Study	Global	Study-wide	78702	C=0.99995	T=0.00005
The PAGE Study	AfricanAmerican	Sub	32516	C=1.00000	T=0.00000
The PAGE Study	Mexican	Sub	10810	C=0.99981	T=0.00019
The PAGE Study	Asian	Sub	8318	C=1.0000	T=0.0000
The PAGE Study	PuertoRican	Sub	7918	C=1.0000	T=0.0000
The PAGE Study	NativeHawaiian	Sub	4534	C=1.0000	T=0.0000
The PAGE Study	Cuban	Sub	4230	C=0.9998	T=0.0002
The PAGE Study	Dominican	Sub	3828	C=1.0000	T=0.0000
The PAGE Study	CentralAmerican	Sub	2450	C=0.9996	T=0.0004
The PAGE Study	SouthAmerican	Sub	1982	C=1.0000	T=0.0000
The PAGE Study	NativeAmerican	Sub	1260	C=1.0000	T=0.0000
The PAGE Study	SouthAsian	Sub	856	C=1.000	T=0.000
14KJPN	JAPANESE	Study-wide	28258	C=0.99993	T=0.00007
8.3KJPN	JAPANESE	Study-wide	16760	C=0.99994	T=0.00006
GO Exome Sequencing Project	Global	Study-wide	13006	C=0.99969	T=0.00031
GO Exome Sequencing Project	European American	Sub	8600	C=0.9997	T=0.0003
GO Exome Sequencing Project	African American	Sub	4406	C=0.9998	T=0.0002
1000Genomes	Global	Study-wide	5008	C=0.9998	T=0.0002
1000Genomes	African	Sub	1322	C=1.0000	T=0.0000
1000Genomes	East Asian	Sub	1008	C=1.0000	T=0.0000
1000Genomes	Europe	Sub	1006	C=1.0000	T=0.0000
1000Genomes	South Asian	Sub	978	C=0.999	T=0.001
1000Genomes	American	Sub	694	C=1.000	T=0.000
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.9997	T=0.0003
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.9997	T=0.0003

Variant Details tab shows known variant placements on genomic sequences: chromosomes (NC_), RefSeqGene, pseudogenes or genomic regions (NG_), and in a separate table: on transcripts (NM_) and protein sequences (NP_). The corresponding transcript and protein locations are listed in adjacent lines, along with molecular consequences from Sequence Ontology. When no protein placement is available, only the transcript is listed. Column "Codon[Amino acid]" shows the actual base change in the format of "Reference > Alternate" allele, including the nucleotide codon change in transcripts, and the amino acid change in proteins, respectively, allowing for known ribosomal slippage sites. To view nucleotides adjacent to the variant use the Genomic View at the bottom of the page - zoom into the sequence until the nucleotides around the variant become visible.

Genomic Placements

Sequence name	Change
GRCh38.p14 chr 18	NC_000018.10:g.36213402C>A
GRCh38.p14 chr 18	NC_000018.10:g.36213402C>T
GRCh37.p13 chr 18	NC_000018.9:g.33793365C>A
GRCh37.p13 chr 18	NC_000018.9:g.33793365C>T
MOCOS RefSeqGene	NG_053177.2:g.30907C>A
MOCOS RefSeqGene	NG_053177.2:g.30907C>T
MOCOS RefSeqGene	NG_053177.1:g.31193C>A
MOCOS RefSeqGene	NG_053177.1:g.31193C>T

Gene: MOCOS, molybdenum cofactor sulfurase (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
MOCOS transcript	NM_017947.4:c.1255C>A	R [CGA] > R [AGA]	Coding Sequence Variant
molybdenum cofactor sulfurase	NP_060417.4:p.Arg419=	R (Arg) > R (Arg)	Synonymous Variant
MOCOS transcript	NM_017947.4:c.1255C>T	R [CGA] > * [TGA]	Coding Sequence Variant
molybdenum cofactor sulfurase	NP_060417.4:p.Arg419Ter	R (Arg) > * (Ter)	Stop Gained

Clinical Significance tab shows a list of clinical significance entries from ClinVar associated with the variation, per allele. Click on the RCV accession (i.e. RCV000001615.2) or Allele ID (i.e. 12274) to access full ClinVar report.

Allele: T (allele ID: 247572 )

ClinVar Accession	Disease Names	Clinical Significance
RCV000239577.6	Xanthinuria type II	Pathogenic

Aliases tab displays HGVS names representing the variant placements and allele changes on genomic, transcript and protein sequences, per allele. HGVS name is an expression for reporting sequence accession and version, sequence type, position, and allele change. The column "Note" can have two values: "diff" means that there is a difference between the reference allele (variation interval) at the placement reported in HGVS name and the reference alleles reported in other HGVS names, and "rev" means that the sequence of this variation interval at the placement reported in HGVS name is in reverse orientation to the sequence(s) of this variation in other HGVS names not labeled as "rev".

Placement	C=	A	T
GRCh38.p14 chr 18	NC_000018.10:g.36213402=	NC_000018.10:g.36213402C>A	NC_000018.10:g.36213402C>T
GRCh37.p13 chr 18	NC_000018.9:g.33793365=	NC_000018.9:g.33793365C>A	NC_000018.9:g.33793365C>T
MOCOS RefSeqGene	NG_053177.2:g.30907=	NG_053177.2:g.30907C>A	NG_053177.2:g.30907C>T
MOCOS RefSeqGene	NG_053177.1:g.31193=	NG_053177.1:g.31193C>A	NG_053177.1:g.31193C>T
MOCOS transcript	NM_017947.4:c.1255=	NM_017947.4:c.1255C>A	NM_017947.4:c.1255C>T
MOCOS transcript	NM_017947.3:c.1255=	NM_017947.3:c.1255C>A	NM_017947.3:c.1255C>T
MOCOS transcript	NM_017947.2:c.1255=	NM_017947.2:c.1255C>A	NM_017947.2:c.1255C>T
molybdenum cofactor sulfurase	NP_060417.4:p.Arg419=	NP_060417.4:p.Arg419=	NP_060417.4:p.Arg419Ter
molybdenum cofactor sulfurase	NP_060417.2:p.Arg419=	NP_060417.2:p.Arg419=	NP_060417.2:p.Arg419Ter

Submissions tab displays variations originally submitted to dbSNP, now supporting this RefSNP cluster (rs). We display Submitter handle, Submission identifier, Date and Build number, when the submission appeared for the first time. Direct submissions to dbSNP have Submission ID in the form of an ss-prefixed number (ss#). Other supporting variations are listed in the table without ss#.

46 SubSNP, 13 Frequency, 1 ClinVar submissions

No	Submitter	Submission ID	Date (Build)
1	NHLBI-ESP	ss342473822	May 09, 2011 (134)
2	EXOME_CHIP	ss491532804	May 04, 2012 (137)
3	CLINSEQ_SNP	ss491749595	May 04, 2012 (137)
4	ILLUMINA	ss780736187	Sep 08, 2015 (146)
5	ILLUMINA	ss783412991	Sep 08, 2015 (146)
6	1000GENOMES	ss1360696582	Aug 21, 2014 (142)
7	EVA_UK10K_ALSPAC	ss1636694273	Apr 01, 2015 (144)
8	EVA_UK10K_TWINSUK	ss1679688306	Apr 01, 2015 (144)
9	EVA_EXAC	ss1693130507	Apr 01, 2015 (144)
10	EVA_DECODE	ss1697695175	Apr 01, 2015 (144)
11	ILLUMINA	ss1752253812	Sep 08, 2015 (146)
12	ILLUMINA	ss1917926921	Feb 12, 2016 (147)
13	ILLUMINA	ss1946497931	Feb 12, 2016 (147)
14	ILLUMINA	ss1959798991	Feb 12, 2016 (147)
15	HUMAN_LONGEVITY	ss2220879200	Dec 20, 2016 (150)
16	GNOMAD	ss2743265332	Nov 08, 2017 (151)
17	GNOMAD	ss2749948364	Nov 08, 2017 (151)
18	GNOMAD	ss2955758985	Nov 08, 2017 (151)
19	AFFY	ss2985116128	Nov 08, 2017 (151)
20	SWEGEN	ss3016397437	Nov 08, 2017 (151)
21	ILLUMINA	ss3021836944	Nov 08, 2017 (151)
22	ILLUMINA	ss3627790869	Oct 12, 2018 (152)
23	ILLUMINA	ss3634702742	Oct 12, 2018 (152)
24	ILLUMINA	ss3640410050	Oct 12, 2018 (152)
25	ILLUMINA	ss3644704347	Oct 12, 2018 (152)
26	OMUKHERJEE_ADBS	ss3646522902	Oct 12, 2018 (152)
27	ILLUMINA	ss3652257981	Oct 12, 2018 (152)
28	ILLUMINA	ss3653888347	Oct 12, 2018 (152)
29	EVA_DECODE	ss3701500107	Jul 13, 2019 (153)
30	ILLUMINA	ss3725670844	Jul 13, 2019 (153)
31	ILLUMINA	ss3744453647	Jul 13, 2019 (153)
32	ILLUMINA	ss3745002900	Jul 13, 2019 (153)
33	PAGE_CC	ss3771967497	Jul 13, 2019 (153)
34	ILLUMINA	ss3772500414	Jul 13, 2019 (153)
35	EVA	ss3825188578	Apr 27, 2020 (154)
36	TOPMED	ss5053755669	Apr 27, 2021 (155)
37	TOPMED	ss5053755670	Apr 27, 2021 (155)
38	TOMMO_GENOMICS	ss5224809830	Apr 27, 2021 (155)
39	EVA	ss5430890656	Oct 16, 2022 (156)
40	TOMMO_GENOMICS	ss5782497949	Oct 16, 2022 (156)
41	EVA	ss5827432664	Oct 16, 2022 (156)
42	EVA	ss5847819251	Oct 16, 2022 (156)
43	EVA	ss5848467715	Oct 16, 2022 (156)
44	EVA	ss5873751242	Oct 16, 2022 (156)
45	EVA	ss5952539918	Oct 16, 2022 (156)
46	EVA	ss5979525315	Oct 16, 2022 (156)
47	1000Genomes	NC_000018.9 - 33793365	Oct 12, 2018 (152)
48	The Avon Longitudinal Study of Parents and Children	NC_000018.9 - 33793365	Oct 12, 2018 (152)
49	ExAC	NC_000018.9 - 33793365	Oct 12, 2018 (152)
50	gnomAD - Genomes	NC_000018.10 - 36213402	Apr 27, 2021 (155)
51	gnomAD - Exomes	NC_000018.9 - 33793365	Jul 13, 2019 (153)
52	GO Exome Sequencing Project	NC_000018.9 - 33793365	Oct 12, 2018 (152)
53	The PAGE Study	NC_000018.10 - 36213402	Jul 13, 2019 (153)
54	8.3KJPN	NC_000018.9 - 33793365	Apr 27, 2021 (155)
55	14KJPN	NC_000018.10 - 36213402	Oct 16, 2022 (156)
56	TopMed Submission ignored due to conflicting rows: Row 269301332 (NC_000018.10:36213401:C:A 4/264690) Row 269301333 (NC_000018.10:36213401:C:T 37/264690)	-	Apr 27, 2021 (155)
57	TopMed Submission ignored due to conflicting rows: Row 269301332 (NC_000018.10:36213401:C:A 4/264690) Row 269301333 (NC_000018.10:36213401:C:T 37/264690)	-	Apr 27, 2021 (155)
58	UK 10K study - Twins	NC_000018.9 - 33793365	Oct 12, 2018 (152)
59	ALFA	NC_000018.10 - 36213402	Apr 27, 2021 (155)
60	ClinVar	RCV000239577.6	Oct 16, 2022 (156)

History tab displays RefSNPs (Associated ID) from previous builds (Build) that now support the current RefSNP, and the dates, when the history was updated for each Associated ID (History Updated).

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss2743265332	NC_000018.9:33793364:C:A	NC_000018.10:36213401:C:A	(self)
2689568668, ss5053755669	NC_000018.10:36213401:C:A	NC_000018.10:36213401:C:A	(self)
ss491749595, ss1697695175	NC_000018.8:32047362:C:T	NC_000018.10:36213401:C:T	(self)
74014991, 41000937, 3600883, 12577292, 1645595, 82779137, 41000937, ss342473822, ss491532804, ss780736187, ss783412991, ss1360696582, ss1636694273, ss1679688306, ss1693130507, ss1752253812, ss1917926921, ss1946497931, ss1959798991, ss2743265332, ss2749948364, ss2955758985, ss2985116128, ss3016397437, ss3021836944, ss3627790869, ss3634702742, ss3640410050, ss3644704347, ss3646522902, ss3652257981, ss3653888347, ss3744453647, ss3745002900, ss3772500414, ss3825188578, ss5224809830, ss5430890656, ss5827432664, ss5847819251, ss5848467715, ss5952539918, ss5979525315	NC_000018.9:33793364:C:T	NC_000018.10:36213401:C:T	(self)
RCV000239577.6, 522152904, 1188966, 116335053, 2689568668, ss2220879200, ss3701500107, ss3725670844, ss3771967497, ss5053755670, ss5782497949, ss5873751242	NC_000018.10:36213401:C:T	NC_000018.10:36213401:C:T	(self)

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

2 citations for rs142150953

PMID	Title	Author	Year	Journal
11302742	Mutation of human molybdenum cofactor sulfurase gene is responsible for classical xanthinuria type II.	Ichida K et al.	2001	Biochemical and biophysical research communications
25967871	Using Next-Generation Sequencing to Identify a Mutation in Human MCSU that is Responsible for Type II Xanthinuria.	Zhou Y et al.	2015	Cellular physiology and biochemistry

The Flanks tab provides retrieving flanking sequences of a SNP on all molecules that have placements.

Genome context:

Select flank length:

Genomic regions, transcripts, and products
Top▲ Help
NCBI Graphical Sequence Viewer display of the genomic region, transcripts and protein products for the reported RefSNP (rs).
Use the zoom option to view the nucleotides around the RefSNP and find other neighboring RefSNPs.
Visit Sequence Viewer for help with navigating inside the display and modifying the selection of displayed data tracks.

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dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

Reference SNP (rs) Report

rs142150953