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dbSNP Short Genetic Variations

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.

rs80356779

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr11:68780662 (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
G>A
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.000034 (9/264690, TOPMED)
A=0.000032 (8/251490, GnomAD_exome)
A=0.000057 (8/140236, GnomAD) (+ 8 more)
A=0.000016 (2/121346, ExAC)
A=0.00018 (5/28258, 14KJPN)
A=0.00018 (3/16758, 8.3KJPN)
A=0.00000 (0/14528, ALFA)
A=0.03 (1/40, GENOME_DK)
G=0.11 (2/18, SGDP_PRJ)
G=0.5 (1/2, Siberian)
A=0.5 (1/2, Siberian)
Clinical Significance
Reported in ClinVar
Gene : Consequence
CPT1A : Missense Variant
Publications
10 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 14528 G=1.00000 A=0.00000
European Sub 9690 G=1.0000 A=0.0000
African Sub 3324 G=1.0000 A=0.0000
African Others Sub 114 G=1.000 A=0.000
African American Sub 3210 G=1.0000 A=0.0000
Asian Sub 112 G=1.000 A=0.000
East Asian Sub 86 G=1.00 A=0.00
Other Asian Sub 26 G=1.00 A=0.00
Latin American 1 Sub 146 G=1.000 A=0.000
Latin American 2 Sub 610 G=1.000 A=0.000
South Asian Sub 98 G=1.00 A=0.00
Other Sub 548 G=1.000 A=0.000


Help

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").

Download
Study Population Group Sample Size Ref Allele Alt Allele
TopMed Global Study-wide 264690 G=0.999966 A=0.000034
gnomAD - Exomes Global Study-wide 251490 G=0.999968 A=0.000032
gnomAD - Exomes European Sub 135414 G=1.000000 A=0.000000
gnomAD - Exomes Asian Sub 49008 G=1.00000 A=0.00000
gnomAD - Exomes American Sub 34592 G=0.99994 A=0.00006
gnomAD - Exomes African Sub 16256 G=1.00000 A=0.00000
gnomAD - Exomes Ashkenazi Jewish Sub 10080 G=1.00000 A=0.00000
gnomAD - Exomes Other Sub 6140 G=0.9990 A=0.0010
gnomAD - Genomes Global Study-wide 140236 G=0.999943 A=0.000057
gnomAD - Genomes European Sub 75934 G=1.00000 A=0.00000
gnomAD - Genomes African Sub 42046 G=0.99998 A=0.00002
gnomAD - Genomes American Sub 13652 G=0.99963 A=0.00037
gnomAD - Genomes Ashkenazi Jewish Sub 3324 G=1.0000 A=0.0000
gnomAD - Genomes East Asian Sub 3132 G=1.0000 A=0.0000
gnomAD - Genomes Other Sub 2148 G=0.9991 A=0.0009
ExAC Global Study-wide 121346 G=0.999984 A=0.000016
ExAC Europe Sub 73338 G=0.99999 A=0.00001
ExAC Asian Sub 25130 G=1.00000 A=0.00000
ExAC American Sub 11568 G=0.99991 A=0.00009
ExAC African Sub 10402 G=1.00000 A=0.00000
ExAC Other Sub 908 G=1.000 A=0.000
14KJPN JAPANESE Study-wide 28258 G=0.99982 A=0.00018
8.3KJPN JAPANESE Study-wide 16758 G=0.99982 A=0.00018
Allele Frequency Aggregator Total Global 14528 G=1.00000 A=0.00000
Allele Frequency Aggregator European Sub 9690 G=1.0000 A=0.0000
Allele Frequency Aggregator African Sub 3324 G=1.0000 A=0.0000
Allele Frequency Aggregator Latin American 2 Sub 610 G=1.000 A=0.000
Allele Frequency Aggregator Other Sub 548 G=1.000 A=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 G=1.000 A=0.000
Allele Frequency Aggregator Asian Sub 112 G=1.000 A=0.000
Allele Frequency Aggregator South Asian Sub 98 G=1.00 A=0.00
The Danish reference pan genome Danish Study-wide 40 G=0.97 A=0.03
SGDP_PRJ Global Study-wide 18 G=0.11 A=0.89
Siberian Global Study-wide 2 G=0.5 A=0.5
Help

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 11 NC_000011.10:g.68780662G>A
GRCh37.p13 chr 11 NC_000011.9:g.68548130G>A
CPT1A RefSeqGene NG_011801.1:g.66270C>T
Gene: CPT1A, carnitine palmitoyltransferase 1A (minus strand)
Molecule type Change Amino acid[Codon] SO Term
CPT1A transcript variant 1 NM_001876.4:c.1436C>T P [CCG] > L [CTG] Coding Sequence Variant
carnitine O-palmitoyltransferase 1, liver isoform isoform 1 NP_001867.2:p.Pro479Leu P (Pro) > L (Leu) Missense Variant
CPT1A transcript variant 2 NM_001031847.3:c.1436C>T P [CCG] > L [CTG] Coding Sequence Variant
carnitine O-palmitoyltransferase 1, liver isoform isoform 2 NP_001027017.1:p.Pro479Leu P (Pro) > L (Leu) Missense Variant
CPT1A transcript variant X1 XM_047426376.1:c.1532C>T P [CCG] > L [CTG] Coding Sequence Variant
carnitine O-palmitoyltransferase 1, liver isoform isoform X1 XP_047282332.1:p.Pro511Leu P (Pro) > L (Leu) Missense Variant
CPT1A transcript variant X2 XM_047426377.1:c.1532C>T P [CCG] > L [CTG] Coding Sequence Variant
carnitine O-palmitoyltransferase 1, liver isoform isoform X2 XP_047282333.1:p.Pro511Leu P (Pro) > L (Leu) Missense Variant
CPT1A transcript variant X3 XM_017017220.2:c.1436C>T P [CCG] > L [CTG] Coding Sequence Variant
carnitine O-palmitoyltransferase 1, liver isoform isoform X3 XP_016872709.1:p.Pro479Leu P (Pro) > L (Leu) Missense Variant
Help

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: A (allele ID: 76552 )
ClinVar Accession Disease Names Clinical Significance
RCV000079911.13 not provided Pathogenic
RCV000551382.11 Carnitine palmitoyl transferase 1A deficiency Pathogenic
RCV000714476.3 CARNITINE PALMITOYLTRANSFERASE IA POLYMORPHISM Benign
RCV000714477.3 CPT1A ARCTIC VARIANT Pathogenic
Help

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 G= A
GRCh38.p14 chr 11 NC_000011.10:g.68780662= NC_000011.10:g.68780662G>A
GRCh37.p13 chr 11 NC_000011.9:g.68548130= NC_000011.9:g.68548130G>A
CPT1A RefSeqGene NG_011801.1:g.66270= NG_011801.1:g.66270C>T
CPT1A transcript variant 1 NM_001876.4:c.1436= NM_001876.4:c.1436C>T
CPT1A transcript variant 1 NM_001876.3:c.1436= NM_001876.3:c.1436C>T
CPT1A transcript variant 2 NM_001031847.3:c.1436= NM_001031847.3:c.1436C>T
CPT1A transcript variant 2 NM_001031847.2:c.1436= NM_001031847.2:c.1436C>T
CPT1A transcript variant X3 XM_017017220.2:c.1436= XM_017017220.2:c.1436C>T
CPT1A transcript variant X3 XM_017017220.1:c.1436= XM_017017220.1:c.1436C>T
CPT1A transcript variant X1 XM_047426376.1:c.1532= XM_047426376.1:c.1532C>T
CPT1A transcript variant X2 XM_047426377.1:c.1532= XM_047426377.1:c.1532C>T
carnitine O-palmitoyltransferase 1, liver isoform isoform 1 NP_001867.2:p.Pro479= NP_001867.2:p.Pro479Leu
carnitine O-palmitoyltransferase 1, liver isoform isoform 2 NP_001027017.1:p.Pro479= NP_001027017.1:p.Pro479Leu
carnitine O-palmitoyltransferase 1, liver isoform isoform X3 XP_016872709.1:p.Pro479= XP_016872709.1:p.Pro479Leu
carnitine O-palmitoyltransferase 1, liver isoform isoform X1 XP_047282332.1:p.Pro511= XP_047282332.1:p.Pro511Leu
carnitine O-palmitoyltransferase 1, liver isoform isoform X2 XP_047282333.1:p.Pro511= XP_047282333.1:p.Pro511Leu
Help

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#.

17 SubSNP, 10 Frequency, 4 ClinVar submissions
No Submitter Submission ID Date (Build)
1 GENEREVIEWS ss184956004 Dec 29, 2009 (131)
2 EVA_GENOME_DK ss1575773353 Apr 01, 2015 (144)
3 EVA_EXAC ss1690515808 Apr 01, 2015 (144)
4 USC_VALOUEV ss2155048310 Dec 20, 2016 (150)
5 HUMAN_LONGEVITY ss2183237695 Dec 20, 2016 (150)
6 GNOMAD ss2739200107 Nov 08, 2017 (151)
7 GNOMAD ss2748681679 Nov 08, 2017 (151)
8 GNOMAD ss2900961634 Nov 08, 2017 (151)
9 EVA_DECODE ss3692003505 Jul 13, 2019 (153)
10 ILLUMINA ss3725251814 Jul 13, 2019 (153)
11 SGDP_PRJ ss3876489041 Apr 26, 2020 (154)
12 TOPMED ss4889200489 Apr 26, 2021 (155)
13 TOMMO_GENOMICS ss5202504810 Apr 26, 2021 (155)
14 EVA ss5400286743 Oct 17, 2022 (156)
15 TOMMO_GENOMICS ss5750549493 Oct 17, 2022 (156)
16 EVA ss5847637986 Oct 17, 2022 (156)
17 EVA ss5979362025 Oct 17, 2022 (156)
18 ExAC NC_000011.9 - 68548130 Oct 12, 2018 (152)
19 The Danish reference pan genome NC_000011.9 - 68548130 Apr 26, 2020 (154)
20 gnomAD - Genomes NC_000011.10 - 68780662 Apr 26, 2021 (155)
21 gnomAD - Exomes NC_000011.9 - 68548130 Jul 13, 2019 (153)
22 SGDP_PRJ NC_000011.9 - 68548130 Apr 26, 2020 (154)
23 Siberian NC_000011.9 - 68548130 Apr 26, 2020 (154)
24 8.3KJPN NC_000011.9 - 68548130 Apr 26, 2021 (155)
25 14KJPN NC_000011.10 - 68780662 Oct 17, 2022 (156)
26 TopMed NC_000011.10 - 68780662 Apr 26, 2021 (155)
27 ALFA NC_000011.10 - 68780662 Apr 26, 2021 (155)
28 ClinVar RCV000079911.13 Oct 17, 2022 (156)
29 ClinVar RCV000551382.11 Oct 17, 2022 (156)
30 ClinVar RCV000714476.3 Oct 17, 2022 (156)
31 ClinVar RCV000714477.3 Oct 17, 2022 (156)
Help

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
782275, 2608908, 8416049, 28506021, 7564664, 60474117, ss1575773353, ss1690515808, ss2155048310, ss2739200107, ss2748681679, ss2900961634, ss3876489041, ss5202504810, ss5400286743, ss5847637986, ss5979362025 NC_000011.9:68548129:G:A NC_000011.10:68780661:G:A (self)
RCV000079911.13, RCV000551382.11, RCV000714476.3, RCV000714477.3, 383044877, 84386597, 104746145, 6889588836, ss184956004, ss2183237695, ss3692003505, ss3725251814, ss4889200489, ss5750549493 NC_000011.10:68780661:G:A NC_000011.10:68780661:G:A (self)
Help

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

10 citations for rs80356779
PMID Title Author Year Journal
11441142 Molecular characterization of L-CPT I deficiency in six patients: insights into function of the native enzyme. Brown NF et al. 2001 Journal of lipid research
20301700 Carnitine Palmitoyltransferase 1A Deficiency. Bennett MJ et al. 1993 GeneReviews(®)
22045927 Genetic polymorphisms in carnitine palmitoyltransferase 1A gene are associated with variation in body composition and fasting lipid traits in Yup'ik Eskimos. Lemas DJ et al. 2012 Journal of lipid research
23757202 Free the data: one laboratory's approach to knowledge-based genomic variant classification and preparation for EMR integration of genomic data. Bean LJ et al. 2013 Human mutation
26010953 Increased missense mutation burden of Fatty Acid metabolism related genes in nunavik inuit population. Zhou S et al. 2015 PloS one
27341449 Identification of Novel Genetic Determinants of Erythrocyte Membrane Fatty Acid Composition among Greenlanders. Andersen MK et al. 2016 PLoS genetics
28611031 CPT1A Missense Mutation Associated With Fatty Acid Metabolism and Reduced Height in Greenlanders. Skotte L et al. 2017 Circulation. Cardiovascular genetics
29433421 The distribution of three candidate cold-resistant SNPs in six minorities in North China. Li Q et al. 2018 BMC genomics
31224529
32561900 Genetic study of the Arctic CPT1A variant suggests that its effect on fatty acid levels is modulated by traditional Inuit diet. Senftleber N et al. 2020 European journal of human genetics
Help

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.

Software version is: 2.0.1.post761+d5e8e07