In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. ClinVar contains an entry for this variant (Variation ID: 2080637). This variant has not been reported in the literature in individuals affected with FAM111A-related conditions. The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This sequence change affects codon 27 of the FAM111A mRNA. It is a 'silent' change, meaning that it does not change the encoded amino acid sequence of the FAM111A protein. This variant also falls at the last nucleotide of exon 3, which is part of the consensus splice site for this exon.
ClinVar Genomic variation as it relates to human health
NM_001312909.2(FAM111A):c.81G>A (p.Pro27=)
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_001312909.2(FAM111A):c.81G>A (p.Pro27=)
Variation ID: 2080637 Accession: VCV002080637.2
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: 11q12.1 11: 59148953 (GRCh38) [ NCBI UCSC ] 11: 58916426 (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 Feb 14, 2024 Aug 4, 2023 - HGVS
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... more HGVS ... less HGVSNucleotide Protein Molecular
consequenceNM_001312909.2:c.81G>A MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_001299838.1:p.Pro27= synonymous NM_001142519.3:c.81G>A NP_001135991.1:p.Pro27= synonymous NM_001142520.3:c.81G>A NP_001135992.1:p.Pro27= synonymous NM_001142521.3:c.81G>A NP_001135993.1:p.Pro27= synonymous NM_001312910.2:c.81G>A NP_001299839.1:p.Pro27= synonymous NM_001312911.2:c.81G>A NP_001299840.1:p.Pro27= synonymous NM_001369457.1:c.81G>A NP_001356386.1:p.Pro27= synonymous NM_001374804.1:c.81G>A NP_001361733.1:p.Pro27= synonymous NM_001374848.1:c.81G>A NP_001361777.1:p.Pro27= synonymous NM_001374849.1:c.81G>A NP_001361778.1:p.Pro27= synonymous NM_001374850.1:c.81G>A NP_001361779.1:p.Pro27= synonymous NM_001374851.1:c.81G>A NP_001361780.1:p.Pro27= synonymous NM_001374852.1:c.81G>A NP_001361781.1:p.Pro27= synonymous NM_001374853.1:c.81G>A NP_001361782.1:p.Pro27= synonymous NM_001374854.1:c.81G>A NP_001361783.1:p.Pro27= synonymous NM_001374855.1:c.81G>A NP_001361784.1:p.Pro27= synonymous NM_001374856.1:c.81G>A NP_001361785.1:p.Pro27= synonymous NM_001374857.1:c.81G>A NP_001361786.1:p.Pro27= synonymous NM_001374858.1:c.81G>A NP_001361787.1:p.Pro27= synonymous NM_001374859.1:c.81G>A NP_001361788.1:p.Pro27= synonymous NM_001374860.1:c.81G>A NP_001361789.1:p.Pro27= synonymous NM_001374861.1:c.81G>A NP_001361790.1:p.Pro27= synonymous NM_001374862.1:c.81G>A NP_001361791.1:p.Pro27= synonymous NM_001374863.1:c.81G>A NP_001361792.1:p.Pro27= synonymous NM_001374864.1:c.81G>A NP_001361793.1:p.Pro27= synonymous NM_001374865.1:c.81G>A NP_001361794.1:p.Pro27= synonymous NM_001374866.1:c.81G>A NP_001361795.1:p.Pro27= synonymous NM_001374867.1:c.81G>A NP_001361796.1:p.Pro27= synonymous NM_001374868.1:c.81G>A NP_001361797.1:p.Pro27= synonymous NM_001374869.1:c.81G>A NP_001361798.1:p.Pro27= synonymous NM_001374870.1:c.81G>A NP_001361799.1:p.Pro27= synonymous NM_022074.4:c.81G>A NP_071357.2:p.Pro27= synonymous NM_198847.3:c.81G>A NP_942144.1:p.Pro27= synonymous NC_000011.10:g.59148953G>A NC_000011.9:g.58916426G>A NG_042835.1:g.11208G>A - Protein change
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- Other names
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- Canonical SPDI
- NC_000011.10:59148952:G:A
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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. |
|||
| FAM111A | - | - |
GRCh38 GRCh37 |
236 | 262 | |
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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Aug 4, 2023 | RCV003002073.3 |
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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|---|---|---|---|---|---|
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Uncertain significance
(Aug 04, 2023)
|
criteria provided, single submitter
Method: clinical testing
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not provided
Affected status: unknown
Allele origin:
germline
|
Labcorp Genetics (formerly Invitae), Labcorp
Accession: SCV003294684.2
First in ClinVar: Feb 07, 2023 Last updated: Feb 14, 2024 |
Comment:
In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant … (more)
In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. ClinVar contains an entry for this variant (Variation ID: 2080637). This variant has not been reported in the literature in individuals affected with FAM111A-related conditions. The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This sequence change affects codon 27 of the FAM111A mRNA. It is a 'silent' change, meaning that it does not change the encoded amino acid sequence of the FAM111A protein. This variant also falls at the last nucleotide of exon 3, which is part of the consensus splice site for this exon. (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:
In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. ClinVar contains an entry for this variant (Variation ID: 2080637). This variant has not been reported in the literature in individuals affected with FAM111A-related conditions. The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This sequence change affects codon 27 of the FAM111A mRNA. It is a 'silent' change, meaning that it does not change the encoded amino acid sequence of the FAM111A protein. This variant also falls at the last nucleotide of exon 3, which is part of the consensus splice site for this exon.
Citations for germline classification of this variant
Help| Title | Author | Journal | Year | Link |
|---|---|---|---|---|
| Aberrant 5' splice sites in human disease genes: mutation pattern, nucleotide structure and comparison of computational tools that predict their utilization. | Buratti E | Nucleic acids research | 2007 | PMID: 17576681 |
| Statistical features of human exons and their flanking regions. | Zhang MQ | Human molecular genetics | 1998 | PMID: 9536098 |
Text-mined citations for this variant ...
HelpRecord last updated Sep 29, 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.