The c.1993C>A (p.P665T) alteration is located in exon 22 (coding exon 22) of the RAP1GAP gene. This alteration results from a C to A substitution at nucleotide position 1993, causing the proline (P) at amino acid position 665 to be replaced by a threonine (T). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.
ClinVar Genomic variation as it relates to human health
NM_002885.4(RAP1GAP):c.1801C>A (p.Pro601Thr)
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)
Help
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_002885.4(RAP1GAP):c.1801C>A (p.Pro601Thr)
Variation ID: 2356369 Accession: VCV002356369.2
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: 1p36.12 1: 21598478 (GRCh38) [ NCBI UCSC ] 1: 21924971 (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 Feb 8, 2023 May 1, 2024 Dec 15, 2022 - HGVS
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... more HGVS ... less HGVSNucleotide Protein Molecular
consequenceNM_002885.4:c.1801C>A MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_002876.2:p.Pro601Thr missense NM_001145657.3:c.1879C>A NP_001139129.1:p.Pro627Thr missense NM_001145658.3:c.1993C>A NP_001139130.1:p.Pro665Thr missense NM_001330383.3:c.2056C>A NP_001317312.1:p.Pro686Thr missense NM_001350524.2:c.2056C>A NP_001337453.1:p.Pro686Thr missense NM_001350525.2:c.1879C>A NP_001337454.1:p.Pro627Thr missense NM_001350526.2:c.1879C>A NP_001337455.1:p.Pro627Thr missense NM_001350527.2:c.1801C>A NP_001337456.1:p.Pro601Thr missense NM_001350528.2:c.1801C>A NP_001337457.1:p.Pro601Thr missense NM_001388200.1:c.2056C>A NP_001375129.1:p.Pro686Thr missense NM_001388201.1:c.2056C>A NP_001375130.1:p.Pro686Thr missense NM_001388202.1:c.1879C>A NP_001375131.1:p.Pro627Thr missense NM_001388203.1:c.1879C>A NP_001375132.1:p.Pro627Thr missense NM_001388204.1:c.1801C>A NP_001375133.1:p.Pro601Thr missense NM_001388205.1:c.2056C>A NP_001375134.1:p.Pro686Thr missense NM_001388206.1:c.2056C>A NP_001375135.1:p.Pro686Thr missense NM_001388207.1:c.2056C>A NP_001375136.1:p.Pro686Thr missense NM_001388208.1:c.2056C>A NP_001375137.1:p.Pro686Thr missense NM_001388209.1:c.2056C>A NP_001375138.1:p.Pro686Thr missense NM_001388210.1:c.1765C>A NP_001375139.1:p.Pro589Thr missense NM_001388211.1:c.2056C>A NP_001375140.1:p.Pro686Thr missense NM_001388212.1:c.2056C>A NP_001375141.1:p.Pro686Thr missense NM_001388213.1:c.2056C>A NP_001375142.1:p.Pro686Thr missense NM_001388214.1:c.2056C>A NP_001375143.1:p.Pro686Thr missense NM_001388215.1:c.1984C>A NP_001375144.1:p.Pro662Thr missense NM_001388216.1:c.1687C>A NP_001375145.1:p.Pro563Thr missense NM_001388217.1:c.1942C>A NP_001375146.1:p.Pro648Thr missense NM_001388218.1:c.1921C>A NP_001375147.1:p.Pro641Thr missense NM_001388219.1:c.1603C>A NP_001375148.1:p.Pro535Thr missense NM_001388220.1:c.1879C>A NP_001375149.1:p.Pro627Thr missense NM_001388221.1:c.1879C>A NP_001375150.1:p.Pro627Thr missense NM_001388222.1:c.1879C>A NP_001375151.1:p.Pro627Thr missense NM_001388223.1:c.1879C>A NP_001375152.1:p.Pro627Thr missense NM_001388224.1:c.1879C>A NP_001375153.1:p.Pro627Thr missense NM_001388225.1:c.1879C>A NP_001375154.1:p.Pro627Thr missense NM_001388226.1:c.1879C>A NP_001375155.1:p.Pro627Thr missense NM_001388227.1:c.1879C>A NP_001375156.1:p.Pro627Thr missense NM_001388228.1:c.1879C>A NP_001375157.1:p.Pro627Thr missense NM_001388229.1:c.1879C>A NP_001375158.1:p.Pro627Thr missense NM_001388230.1:c.1879C>A NP_001375159.1:p.Pro627Thr missense NM_001388231.1:c.1852C>A NP_001375160.1:p.Pro618Thr missense NM_001388233.1:c.1840C>A NP_001375162.1:p.Pro614Thr missense NM_001388234.1:c.1828C>A NP_001375163.1:p.Pro610Thr missense NM_001388235.1:c.1828C>A NP_001375164.1:p.Pro610Thr missense NM_001388236.1:c.1801C>A NP_001375165.1:p.Pro601Thr missense NM_001388237.1:c.1801C>A NP_001375166.1:p.Pro601Thr missense NM_001388238.1:c.1801C>A NP_001375167.1:p.Pro601Thr missense NM_001388239.1:c.1801C>A NP_001375168.1:p.Pro601Thr missense NM_001388240.1:c.1801C>A NP_001375169.1:p.Pro601Thr missense NM_001388241.1:c.1801C>A NP_001375170.1:p.Pro601Thr missense NM_001388242.1:c.1801C>A NP_001375171.1:p.Pro601Thr missense NM_001388243.1:c.1801C>A NP_001375172.1:p.Pro601Thr missense NM_001388244.1:c.1795C>A NP_001375173.1:p.Pro599Thr missense NM_001388245.1:c.1801C>A NP_001375174.1:p.Pro601Thr missense NM_001388246.1:c.1801C>A NP_001375175.1:p.Pro601Thr missense NM_001388247.1:c.1801C>A NP_001375176.1:p.Pro601Thr missense NM_001388248.1:c.1801C>A NP_001375177.1:p.Pro601Thr missense NM_001388249.1:c.1801C>A NP_001375178.1:p.Pro601Thr missense NM_001388250.1:c.1801C>A NP_001375179.1:p.Pro601Thr missense NM_001388251.1:c.1765C>A NP_001375180.1:p.Pro589Thr missense NM_001388252.1:c.1765C>A NP_001375181.1:p.Pro589Thr missense NM_001388253.1:c.1750C>A NP_001375182.1:p.Pro584Thr missense NM_001388254.1:c.1765C>A NP_001375183.1:p.Pro589Thr missense NM_001388255.1:c.1801C>A NP_001375184.1:p.Pro601Thr missense NM_001388256.1:c.1729C>A NP_001375185.1:p.Pro577Thr missense NM_001388258.1:c.1729C>A NP_001375187.1:p.Pro577Thr missense NM_001388259.1:c.1750C>A NP_001375188.1:p.Pro584Thr missense NM_001388261.1:c.1687C>A NP_001375190.1:p.Pro563Thr missense NM_001388263.1:c.1687C>A NP_001375192.1:p.Pro563Thr missense NM_001388264.1:c.1687C>A NP_001375193.1:p.Pro563Thr missense NM_001388266.1:c.1687C>A NP_001375195.1:p.Pro563Thr missense NM_001388267.1:c.1687C>A NP_001375196.1:p.Pro563Thr missense NM_001388269.1:c.1663C>A NP_001375198.1:p.Pro555Thr missense NM_001388270.1:c.1687C>A NP_001375199.1:p.Pro563Thr missense NM_001388273.1:c.1687C>A NP_001375202.1:p.Pro563Thr missense NM_001388276.1:c.1591C>A NP_001375205.1:p.Pro531Thr missense NM_001388279.1:c.1336C>A NP_001375208.1:p.Pro446Thr missense NM_001388280.1:c.1336C>A NP_001375209.1:p.Pro446Thr missense NM_001388281.1:c.1477C>A NP_001375210.1:p.Pro493Thr missense NM_001388282.1:c.1684C>A NP_001375211.1:p.Pro562Thr missense NM_001388283.1:c.1801C>A NP_001375212.1:p.Pro601Thr missense NM_001388284.1:c.1801C>A NP_001375213.1:p.Pro601Thr missense NM_001388285.1:c.1801C>A NP_001375214.1:p.Pro601Thr missense NM_001388286.1:c.1804C>A NP_001375215.1:p.Pro602Thr missense NM_001388287.1:c.1879C>A NP_001375216.1:p.Pro627Thr missense NM_001388288.1:c.1879C>A NP_001375217.1:p.Pro627Thr missense NM_001388289.1:c.1993C>A NP_001375218.1:p.Pro665Thr missense NM_001388290.1:c.1987C>A NP_001375219.1:p.Pro663Thr missense NM_001388291.1:c.1999C>A NP_001375220.1:p.Pro667Thr missense NM_001388292.1:c.2071C>A NP_001375221.1:p.Pro691Thr missense NM_001388293.1:c.2071C>A NP_001375222.1:p.Pro691Thr missense NM_001388294.1:c.2248C>A NP_001375223.1:p.Pro750Thr missense NM_001388295.1:c.2248C>A NP_001375224.1:p.Pro750Thr missense NM_001388296.1:c.1993C>A NP_001375225.1:p.Pro665Thr missense NR_170899.1:n.1855C>A non-coding transcript variant NR_170900.1:n.2131C>A non-coding transcript variant NR_170901.1:n.2053C>A non-coding transcript variant NR_170902.1:n.2308C>A non-coding transcript variant NR_170903.1:n.2046C>A non-coding transcript variant NR_170904.1:n.1939C>A non-coding transcript variant NR_170905.1:n.2243C>A non-coding transcript variant NR_170906.1:n.2415C>A non-coding transcript variant NR_170907.1:n.2217C>A non-coding transcript variant NR_170908.1:n.2160C>A non-coding transcript variant NR_170909.1:n.2272C>A non-coding transcript variant NR_170910.1:n.2129C>A non-coding transcript variant NR_170911.1:n.1903C>A non-coding transcript variant NR_170912.1:n.2498C>A non-coding transcript variant NR_170913.1:n.2391C>A non-coding transcript variant NR_170914.1:n.2610C>A non-coding transcript variant NR_170915.1:n.2095C>A non-coding transcript variant NR_170916.1:n.2057C>A non-coding transcript variant NR_170920.1:n.2238C>A non-coding transcript variant NR_170921.1:n.2080C>A non-coding transcript variant NR_170923.1:n.2069C>A non-coding transcript variant NR_170924.1:n.1955C>A non-coding transcript variant NR_170925.1:n.3011C>A non-coding transcript variant NR_170926.1:n.1845C>A non-coding transcript variant NR_170927.1:n.2685C>A non-coding transcript variant NR_170928.1:n.2737C>A non-coding transcript variant NR_170929.1:n.2469C>A non-coding transcript variant NC_000001.11:g.21598478G>T NC_000001.10:g.21924971G>T NG_029807.1:g.75886C>A - Protein change
- P589T, P610T, P618T, P665T, P667T, P691T, P446T, P563T, P584T, P602T, P663T, P686T, P750T, P493T, P531T, P535T, P562T, P577T, P601T, P614T, P662T, P555T, P599T, P627T, P641T, P648T
- Other names
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- Canonical SPDI
- NC_000001.11:21598477:G:T
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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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| RAP1GAP | - | - |
GRCh38 GRCh37 |
37 | 53 | |
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. |
|---|---|---|---|---|
| Uncertain significance (1) |
criteria provided, single submitter
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Dec 15, 2022 | RCV004190931.1 |
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
(Dec 15, 2022)
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criteria provided, single submitter
Method: clinical testing
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not specified
Affected status: unknown
Allele origin:
germline
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Ambry Genetics
Accession: SCV003686697.2
First in ClinVar: Feb 07, 2023 Last updated: May 01, 2024 |
Comment:
The c.1993C>A (p.P665T) alteration is located in exon 22 (coding exon 22) of the RAP1GAP gene. This alteration results from a C to A substitution … (more)
The c.1993C>A (p.P665T) alteration is located in exon 22 (coding exon 22) of the RAP1GAP gene. This alteration results from a C to A substitution at nucleotide position 1993, causing the proline (P) at amino acid position 665 to be replaced by a threonine (T). Based on insufficient or conflicting evidence, 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 c.1993C>A (p.P665T) alteration is located in exon 22 (coding exon 22) of the RAP1GAP gene. This alteration results from a C to A substitution at nucleotide position 1993, causing the proline (P) at amino acid position 665 to be replaced by a threonine (T). Based on insufficient or conflicting evidence, 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 Nov 25, 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.