FAM20A p.Leu13Leu

Variant names:

• chr17-68600627-G-G
• NM_017565.4:c.

Your query was ambiguous. Multiple possible variants found:

• chr17-68600628--
• chr17-68600630-G-A
• chr17-68600628-C-A
• chr17-68600628-C-G
• chr17-68600628-C-T
• chr17-68600628-CAG-TAA

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_017565.4(FAM20A):​c. variant causes a exon region change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 32)
• Consequence: FAM20A NM_017565.4 exon_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.76
• Publications: 0 publications found

Genes affected

FAM20A (HGNC:23015): (FAM20A golgi associated secretory pathway pseudokinase) This locus encodes a protein that is likely secreted and may function in hematopoiesis. A mutation at this locus has been associated with amelogenesis imperfecta and gingival hyperplasia syndrome. Alternatively spliced transcript variants have been identified. [provided by RefSeq, Aug 2011]

LINC01482 (HGNC:51128): (long intergenic non-protein coding RNA 1482)

ACMG classification

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_017565.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FAM20A	NM_017565.4	MANE Select	c.		exon_region	Exon 1 of 11	NP_060035.2	Q96MK3
	FAM20A	NM_001243746.2		c.		exon_region	Exon 1 of 12	NP_001230675.1
	FAM20A	NM_001243746.2		c.		5_prime_UTR	Exon 1 of 12	NP_001230675.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FAM20A	ENST00000592554.2	TSL:1 MANE Select	c.		exon_region	Exon 1 of 11	ENSP00000468308.1	Q96MK3
	FAM20A	ENST00000882126.1		c.		exon_region	Exon 1 of 12	ENSP00000552185.1
	FAM20A	ENST00000882123.1		c.		exon_region	Exon 1 of 10	ENSP00000552182.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 33

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		1.8

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

hg19: chr17-66596768;