This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.
ClinVar Genomic variation as it relates to human health
NM_024956.4(TMEM62):c.1579A>T (p.Ile527Leu)
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.
Likely benign
1
criteria provided, single submitter
Somatic
No data submitted for somatic clinical impact
Somatic
No data submitted for oncogenicity
Variant Details
- Identifiers
-
NM_024956.4(TMEM62):c.1579A>T (p.Ile527Leu)
Variation ID: 2493280 Accession: VCV002493280.2
- Type and length
-
single nucleotide variant, 1 bp
- Location
-
Cytogenetic: 15q15.2 15: 43181273 (GRCh38) [ NCBI UCSC ] 15: 43473471 (GRCh37) [ NCBI UCSC ]
- Timeline in ClinVar
-
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 Apr 15, 2023 May 1, 2024 Mar 2, 2023 - HGVS
-
... more HGVS ... less HGVSNucleotide Protein Molecular
consequenceNM_024956.4:c.1579A>T MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_079232.3:p.Ile527Leu missense NM_001347004.1:c.1189A>T NP_001333933.1:p.Ile397Leu missense NM_001347005.2:c.1189A>T NP_001333934.1:p.Ile397Leu missense NM_001347006.2:c.1189A>T NP_001333935.1:p.Ile397Leu missense NM_001347007.2:c.1189A>T NP_001333936.1:p.Ile397Leu missense NM_001347008.1:c.1183A>T NP_001333937.1:p.Ile395Leu missense NM_001347009.1:c.1183A>T NP_001333938.1:p.Ile395Leu missense NM_001347010.2:c.1183A>T NP_001333939.1:p.Ile395Leu missense NM_001347011.2:c.1183A>T NP_001333940.1:p.Ile395Leu missense NM_001347012.2:c.1183A>T NP_001333941.1:p.Ile395Leu missense NM_001347013.2:c.1183A>T NP_001333942.1:p.Ile395Leu missense NM_001347014.1:c.1084A>T NP_001333943.1:p.Ile362Leu missense NM_001347015.2:c.1084A>T NP_001333944.1:p.Ile362Leu missense NM_001347016.2:c.1084A>T NP_001333945.1:p.Ile362Leu missense NM_001347017.2:c.1078A>T NP_001333946.1:p.Ile360Leu missense NM_001347018.2:c.1078A>T NP_001333947.1:p.Ile360Leu missense NM_001347019.1:c.964A>T NP_001333948.1:p.Ile322Leu missense NM_001347020.2:c.964A>T NP_001333949.1:p.Ile322Leu missense NM_001347021.2:c.964A>T NP_001333950.1:p.Ile322Leu missense NM_001347023.2:c.964A>T NP_001333952.1:p.Ile322Leu missense NM_001347024.1:c.859A>T NP_001333953.1:p.Ile287Leu missense NM_001347025.1:c.859A>T NP_001333954.1:p.Ile287Leu missense NM_001347026.2:c.859A>T NP_001333955.1:p.Ile287Leu missense NM_001347027.2:c.859A>T NP_001333956.1:p.Ile287Leu missense NM_001347028.2:c.859A>T NP_001333957.1:p.Ile287Leu missense NM_001347029.2:c.859A>T NP_001333958.1:p.Ile287Leu missense NM_001347030.1:c.817A>T NP_001333959.1:p.Ile273Leu missense NM_001347031.2:c.1207A>T NP_001333960.1:p.Ile403Leu missense NM_001347032.2:c.1474A>T NP_001333961.1:p.Ile492Leu missense NM_001347033.2:c.1312A>T NP_001333962.1:p.Ile438Leu missense NM_001347034.2:c.850A>T NP_001333963.1:p.Ile284Leu missense NR_144541.1:n.1503A>T non-coding transcript variant NR_144542.2:n.1612A>T non-coding transcript variant NR_144543.2:n.1644A>T non-coding transcript variant NR_144544.2:n.1566A>T non-coding transcript variant NC_000015.10:g.43181273A>T NC_000015.9:g.43473471A>T - Protein change
- I284L, I360L, I403L, I492L, I322L, I362L, I527L, I273L, I287L, I395L, I397L, I438L
- Other names
- -
- Canonical SPDI
- NC_000015.10:43181272:A:T
-
Functional
consequence HelpThe effect of the variant on RNA or protein function, based on experimental evidence from submitters.
- -
-
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.
- -
-
Allele frequency
Help
The frequency of the allele represented by this VCV record.
- -
- 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. |
|||
| TMEM62 | - | - | - |
GRCh38 GRCh37 |
31 | 58 |
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. |
|---|---|---|---|---|
| Likely benign (1) |
criteria provided, single submitter
|
Mar 2, 2023 | RCV004282788.1 |
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. |
|
|---|---|---|---|---|---|
|
Likely benign
(Mar 02, 2023)
|
criteria provided, single submitter
Method: clinical testing
|
not specified
Affected status: unknown
Allele origin:
germline
|
Ambry Genetics
Accession: SCV003901633.2
First in ClinVar: Apr 15, 2023 Last updated: May 01, 2024 |
Comment:
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of … (more)
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. (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:
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.
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.