VCV002390288.2 - ClinVar

NM_001385994.1(FAM13B):c.1553G>A (p.Gly518Glu)

Germline

Classification

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)

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

criteria provided, single submitter

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

NM_001385994.1(FAM13B):c.1553G>A (p.Gly518Glu)

Variation ID: 2390288 Accession: VCV002390288.2

Type and length

single nucleotide variant, 1 bp

Location

Cytogenetic: 5q31.2 5: 137954331 (GRCh38) [ NCBI UCSC ] 5: 137290020 (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	Feb 8, 2023	May 1, 2024	Jul 20, 2022

HGVS

Nucleotide	Protein	Molecular consequence
NM_001385994.1:c.1553G>A MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.	NP_001372923.1:p.Gly518Glu	missense
NM_001101800.3:c.1487G>A	NP_001095270.1:p.Gly496Glu	missense
NM_001101801.3:c.1199G>A	NP_001095271.1:p.Gly400Glu	missense
NM_001385866.1:c.1133G>A	NP_001372795.1:p.Gly378Glu	missense
NM_001385867.1:c.1487G>A	NP_001372796.1:p.Gly496Glu	missense
NM_001385868.1:c.1553G>A	NP_001372797.1:p.Gly518Glu	missense
NM_001385869.1:c.761G>A	NP_001372798.1:p.Gly254Glu	missense
NM_001385870.1:c.1397G>A	NP_001372799.1:p.Gly466Glu	missense
NM_001385872.1:c.1199G>A	NP_001372801.1:p.Gly400Glu	missense
NM_001385873.1:c.1199G>A	NP_001372802.1:p.Gly400Glu	missense
NM_001385874.1:c.1397G>A	NP_001372803.1:p.Gly466Glu	missense
NM_001385921.1:c.1487G>A	NP_001372850.1:p.Gly496Glu	missense
NM_001385976.1:c.1199G>A	NP_001372905.1:p.Gly400Glu	missense
NM_001385977.1:c.1133G>A	NP_001372906.1:p.Gly378Glu	missense
NM_001385978.1:c.917G>A	NP_001372907.1:p.Gly306Glu	missense
NM_001385979.1:c.1133G>A	NP_001372908.1:p.Gly378Glu	missense
NM_001385980.1:c.1553G>A	NP_001372909.1:p.Gly518Glu	missense
NM_001385991.1:c.1487G>A	NP_001372920.1:p.Gly496Glu	missense
NM_001385992.1:c.1487G>A	NP_001372921.1:p.Gly496Glu	missense
NM_001385995.1:c.1133G>A	NP_001372924.1:p.Gly378Glu	missense
NM_001385996.1:c.917G>A	NP_001372925.1:p.Gly306Glu	missense
NM_001385997.1:c.1331G>A	NP_001372926.1:p.Gly444Glu	missense
NM_001385998.1:c.707G>A	NP_001372927.1:p.Gly236Glu	missense
NM_001385999.1:c.1199G>A	NP_001372928.1:p.Gly400Glu	missense
NM_016603.4:c.1487G>A	NP_057687.2:p.Gly496Glu	missense
NR_169814.1:n.1795G>A		non-coding transcript variant
NR_169815.1:n.1788G>A		non-coding transcript variant
NR_169822.1:n.1967G>A		non-coding transcript variant
NR_169823.1:n.1987G>A		non-coding transcript variant
NR_169824.1:n.1730G>A		non-coding transcript variant
NR_169825.1:n.2053G>A		non-coding transcript variant
NR_169826.1:n.1987G>A		non-coding transcript variant
NC_000005.10:g.137954331C>T
NC_000005.9:g.137290020C>T

... more HGVS ... less HGVS

Protein change

G236E, G306E, G400E, G496E, G518E, G254E, G378E, G444E, G466E

Other names

Canonical SPDI

NC_000005.10:137954330:C:T

Functional consequence Help The effect of the variant on RNA or protein function, based on experimental evidence from submitters.

Global minor allele frequency (GMAF) Help The 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

VarSome

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
Gene	OMIM	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.
FAM13B		-	-	GRCh38 GRCh37	38	67
LOC129389374	-	-	-	GRCh38	-	13

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.
not specified	Uncertain significance (1)	criteria provided, single submitter	Jul 20, 2022	RCV004229572.1

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.
Uncertain significance (Jul 20, 2022)	criteria provided, single submitter (Ambry Variant Classification Scheme 2023) Method: clinical testing	not specified Affected status: unknown Allele origin: germline	Ambry Genetics Accession: SCV003729871.2 First in ClinVar: Feb 07, 2023 Last updated: May 01, 2024	Comment: The c.1487G>A (p.G496E) alteration is located in exon 14 (coding exon 12) of the FAM13B gene. This alteration results from a G to A substitution … (more) The c.1487G>A (p.G496E) alteration is located in exon 14 (coding exon 12) of the FAM13B gene. This alteration results from a G to A substitution at nucleotide position 1487, causing the glycine (G) at amino acid position 496 to be replaced by a glutamic acid (E). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. (less)

Comment:

The c.1487G>A (p.G496E) alteration is located in exon 14 (coding exon 12) of the FAM13B gene. This alteration results from a G to A substitution at nucleotide position 1487, causing the glycine (G) at amino acid position 496 to be replaced by a glutamic acid (E). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.

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:

Citations for germline classification of this variant

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 ...

Record last updated Nov 10, 2024

ClinVar Genomic variation as it relates to human health

NM_001385994.1(FAM13B):c.1553G>A (p.Gly518Glu)

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for this variant ...