NM_001320033.2:c.214_216delCTCinsTTT

Variant names:

• chr3-38306240-CTC-TTT
• NM_001320033.2:c.214_216delCTCinsTTT
• SLC22A14 p.Leu72Phe

Variant summary

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

The NM_001320033.2(SLC22A14):​c.214_216delCTCinsTTT​(p.Leu72Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. It is difficult to determine the true allele frequency of this variant because it is of type MNV, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in the same amino acid substitution has been previously reported as Uncertain significance in ClinVar.

• Frequency: Genomes: not found (cov: 32)
• Consequence: SLC22A14 NM_001320033.2 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.36
• Publications: 0 publications found

Genes affected

SLC22A14 (HGNC:8495): (solute carrier family 22 member 14) This gene encodes a member of the organic-cation transporter family. It is located in a gene cluster with another member of the family, organic cation transporter like 3. The encoded protein is a transmembrane protein which is thought to transport small molecules and since this protein is conserved among several species, it is suggested to have a fundamental role in mammalian systems. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Feb 2016]

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001320033.2. 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
	SLC22A14	NM_001320033.2	MANE Select	c.214_216delCTCinsTTT	p.Leu72Phe	missense	N/A	NP_001306962.1	Q9Y267
	SLC22A14	NM_004803.4		c.214_216delCTCinsTTT	p.Leu72Phe	missense	N/A	NP_004794.2	Q9Y267

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC22A14	ENST00000448498.6	TSL:1 MANE Select	c.214_216delCTCinsTTT	p.Leu72Phe	missense	N/A	ENSP00000396283.1	Q9Y267
	SLC22A14	ENST00000273173.4	TSL:1	c.214_216delCTCinsTTT	p.Leu72Phe	missense	N/A	ENSP00000273173.4	Q9Y267
	SLC22A14	ENST00000466887.5	TSL:4	c.-119-64_-119-62delCTCinsTTT		intron	N/A	ENSP00000442528.1	F5H7H1

Frequencies

GnomAD3 genomes Cov.: 32

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		3.4

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: chr3-38347731;