The p.N1229T variant (also known as c.3686A>C), located in coding exon 8 of the MSH6 gene, results from an A to C substitution at nucleotide position 3686. The asparagine at codon 1229 is replaced by threonine, an amino acid with similar properties. This amino acid position is conserved. In addition, this alteration is predicted to be tolerated by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.
ClinVar Genomic variation as it relates to human health
NM_000179.3(MSH6):c.3686A>C (p.Asn1229Thr)
Germline
Classification
Help
The aggregate germline classification for this variant, typically for a monogenic or Mendelian disorder as in the ACMG/AMP guidelines, or for response to a drug. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the aggregate classification.
(1)
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Stars represent the aggregate review status, or the level of review supporting the aggregate germline classification for this VCV record. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. The number of submissions which contribute to this review status is shown in parentheses.
Uncertain significance
1
criteria provided, single submitter
Somatic
No data submitted for somatic clinical impact
Somatic
No data submitted for oncogenicity
Variant Details
- Identifiers
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NM_000179.3(MSH6):c.3686A>C (p.Asn1229Thr)
Variation ID: 1733920 Accession: VCV001733920.2
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: 2p16.3 2: 47806243 (GRCh38) [ NCBI UCSC ] 2: 48033382 (GRCh37) [ NCBI UCSC ]
- Timeline in ClinVar
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First in ClinVar Help The date this variant first appeared in ClinVar with each type of classification.
Last submission Help The date of the most recent submission for each type of classification for this variant.
Last evaluated Help The most recent date that a submitter evaluated this variant for each type of classification.
Germline Nov 29, 2022 May 1, 2024 Jan 16, 2022 - HGVS
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... more HGVS ... less HGVSNucleotide Protein Molecular
consequenceNM_000179.3:c.3686A>C MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_000170.1:p.Asn1229Thr missense NM_001281492.2:c.3296A>C NP_001268421.1:p.Asn1099Thr missense NM_001281493.2:c.2780A>C NP_001268422.1:p.Asn927Thr missense NM_001281494.2:c.2780A>C NP_001268423.1:p.Asn927Thr missense NM_001406795.1:c.3782A>C NP_001393724.1:p.Asn1261Thr missense NM_001406796.1:c.3686A>C NP_001393725.1:p.Asn1229Thr missense NM_001406797.1:c.3389A>C NP_001393726.1:p.Asn1130Thr missense NM_001406798.1:c.3512A>C NP_001393727.1:p.Asn1171Thr missense NM_001406799.1:c.3161A>C NP_001393728.1:p.Asn1054Thr missense NM_001406800.1:c.3686A>C NP_001393729.1:p.Asn1229Thr missense NM_001406801.1:c.3389A>C NP_001393730.1:p.Asn1130Thr missense NM_001406802.1:c.3782A>C NP_001393731.1:p.Asn1261Thr missense NM_001406803.1:c.2822A>C NP_001393732.1:p.Asn941Thr missense NM_001406804.1:c.3608A>C NP_001393733.1:p.Asn1203Thr missense NM_001406805.1:c.3389A>C NP_001393734.1:p.Asn1130Thr missense NM_001406806.1:c.3161A>C NP_001393735.1:p.Asn1054Thr missense NM_001406807.1:c.3161A>C NP_001393736.1:p.Asn1054Thr missense NM_001406808.1:c.3686A>C NP_001393737.1:p.Asn1229Thr missense NM_001406809.1:c.3686A>C NP_001393738.1:p.Asn1229Thr missense NM_001406811.1:c.2780A>C NP_001393740.1:p.Asn927Thr missense NM_001406812.1:c.2780A>C NP_001393741.1:p.Asn927Thr missense NM_001406813.1:c.3692A>C NP_001393742.1:p.Asn1231Thr missense NM_001406814.1:c.2780A>C NP_001393743.1:p.Asn927Thr missense NM_001406815.1:c.2780A>C NP_001393744.1:p.Asn927Thr missense NM_001406816.1:c.2780A>C NP_001393745.1:p.Asn927Thr missense NM_001406817.1:c.2120A>C NP_001393746.1:p.Asn707Thr missense NM_001406818.1:c.3389A>C NP_001393747.1:p.Asn1130Thr missense NM_001406819.1:c.3389A>C NP_001393748.1:p.Asn1130Thr missense NM_001406820.1:c.3389A>C NP_001393749.1:p.Asn1130Thr missense NM_001406821.1:c.3389A>C NP_001393750.1:p.Asn1130Thr missense NM_001406822.1:c.3389A>C NP_001393751.1:p.Asn1130Thr missense NM_001406823.1:c.2780A>C NP_001393752.1:p.Asn927Thr missense NM_001406824.1:c.3389A>C NP_001393753.1:p.Asn1130Thr missense NM_001406825.1:c.3389A>C NP_001393754.1:p.Asn1130Thr missense NM_001406826.1:c.3518A>C NP_001393755.1:p.Asn1173Thr missense NM_001406827.1:c.3389A>C NP_001393756.1:p.Asn1130Thr missense NM_001406828.1:c.3389A>C NP_001393757.1:p.Asn1130Thr missense NM_001406829.1:c.2780A>C NP_001393758.1:p.Asn927Thr missense NM_001406830.1:c.3389A>C NP_001393759.1:p.Asn1130Thr missense NM_001406831.1:c.467A>C NP_001393760.1:p.Asn156Thr missense NM_001406832.1:c.533A>C NP_001393761.1:p.Asn178Thr missense NM_001407362.1:c.1631A>C NP_001394291.1:p.Asn544Thr missense NR_176256.1:n.2616A>C NR_176257.1:n.3947A>C NR_176258.1:n.3876A>C NR_176259.1:n.3775A>C NR_176260.1:n.1720A>C NR_176261.1:n.3657A>C NC_000002.12:g.47806243A>C NC_000002.11:g.48033382A>C NG_007111.1:g.28097A>C NG_008397.1:g.104433T>G LRG_219:g.28097A>C LRG_219t1:c.3686A>C LRG_219p1:p.Asn1229Thr - Protein change
- N1173T, N1261T, N178T, N544T, N1130T, N1171T, N156T, N1229T, N941T, N1054T, N1099T, N1203T, N1231T, N707T, N927T
- Other names
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- Canonical SPDI
- NC_000002.12:47806242:A:C
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Functional
consequence HelpThe effect of the variant on RNA or protein function, based on experimental evidence from submitters.
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Global minor allele
frequency (GMAF) HelpThe global minor allele frequency calculated by the 1000 Genomes Project. The minor allele at this location is indicated in parentheses and may be different from the allele represented by this VCV record.
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Allele frequency
Help
The frequency of the allele represented by this VCV record.
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- Links
Genes
| Gene | OMIM | ClinGen Gene Dosage Sensitivity Curation |
Variation Viewer
Help
Links to Variation Viewer, a genome browser to view variation data from NCBI databases. |
Related variants | ||
|---|---|---|---|---|---|---|
| HI score
Help
The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
TS score
Help
The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
Within gene
Help
The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants. |
All
Help
The number of variants in ClinVar for this gene, including smaller variants within the gene and larger CNVs that overlap or fully contain the gene. |
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| MSH6 | Sufficient evidence for dosage pathogenicity | No evidence available |
GRCh38 GRCh37 |
9159 | 9475 | |
Conditions - Germline
| Condition
Help
The condition for this variant-condition (RCV) record in ClinVar. |
Classification
Help
The aggregate germline classification for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to this aggregate classification is shown in parentheses. (# of submissions) |
Review status
Help
The aggregate review status for this variant-condition (RCV) record in ClinVar. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. |
Last evaluated
Help
The most recent date that a submitter evaluated this variant for the condition. |
Variation/condition record
Help
The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page. |
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| Uncertain significance (1) |
criteria provided, single submitter
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Jan 16, 2022 | RCV002457438.2 |
Submissions - Germline
| Classification
Help
The submitted germline classification for each SCV record. (Last evaluated) |
Review status
Help
Stars represent the review status, or the level of review supporting the submitted (SCV) record. This value is calculated by NCBI based on data from the submitter. Read our rules for calculating the review status. This column also includes a link to the submitter’s assertion criteria if provided, and the collection method. (Assertion criteria) |
Condition
Help
The condition for the classification, provided by the submitter for this submitted (SCV) record. This column also includes the affected status and allele origin of individuals observed with this variant. |
Submitter
Help
The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar. |
More information
Help
This column includes more information supporting the classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter. |
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Uncertain significance
(Jan 16, 2022)
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criteria provided, single submitter
Method: clinical testing
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Hereditary cancer-predisposing syndrome
Affected status: unknown
Allele origin:
germline
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Ambry Genetics
Accession: SCV002615284.2
First in ClinVar: Nov 29, 2022 Last updated: May 01, 2024 |
Comment:
The p.N1229T variant (also known as c.3686A>C), located in coding exon 8 of the MSH6 gene, results from an A to C substitution at nucleotide … (more)
The p.N1229T variant (also known as c.3686A>C), located in coding exon 8 of the MSH6 gene, results from an A to C substitution at nucleotide position 3686. The asparagine at codon 1229 is replaced by threonine, an amino acid with similar properties. This amino acid position is conserved. In addition, this alteration is predicted to be tolerated by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear. (less)
|
Comment:
Germline Functional Evidence
| There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar. |
Comment:
The p.N1229T variant (also known as c.3686A>C), located in coding exon 8 of the MSH6 gene, results from an A to C substitution at nucleotide position 3686. The asparagine at codon 1229 is replaced by threonine, an amino acid with similar properties. This amino acid position is conserved. In addition, this alteration is predicted to be tolerated by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.
Citations for germline classification of this variant
Help| There are no citations for germline classification of this variant in ClinVar. If you know of citations for this variation, please consider submitting that information to ClinVar. |
Text-mined citations for this variant ...
HelpRecord last updated May 01, 2024
This date represents the last time this VCV record was updated. The update may be due to an update to one of the included submitted records (SCVs), or due to an update that ClinVar made to the variant such as adding HGVS expressions or a rs number. So this date may be different from the date of the “most recent submission” reported at the top of this page.