3-170467058-CTCTGGAGAG-C

Variant names:

• chr3-170467058-CTCTGGAGAG-C
• NM_020949.3:c.2304_2312delCTCTCCAGA

Variant summary

Our verdict is Uncertain significance. The variant received 4 ACMG points: 4P and 0B. PM2 PM4

The NM_020949.3(SLC7A14):​c.2304_2312delCTCTCCAGA​(p.Tyr768_Glu771delinsTer) variant causes a stop gained, disruptive inframe deletion change. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: SLC7A14 NM_020949.3 stop_gained, disruptive_inframe_deletion
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 6.39
• Publications: 0 publications found

Genes affected

SLC7A14 (HGNC:29326): (solute carrier family 7 member 14) This gene is predicted to encode a glycosylated, cationic amino acid transporter protein with 14 transmembrane domains. This gene is primarily expressed in skin fibroblasts, neural tissue, and primary endothelial cells and its protein is predicted to mediate lysosomal uptake of cationic amino acids. Mutations in this gene are associated with autosomal recessive retinitis pigmentosa. In mice, this gene is expressed in the photoreceptor layer of the retina where its expression increases over the course of retinal development and persists in the mature retina. [provided by RefSeq, Apr 2014]

ENSG00000285218 (HGNC:):

SLC7A14-AS1 (HGNC:54092): (SLC7A14 antisense RNA 1)

ACMG classification

Our verdict: Uncertain_significance. The variant received 4 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PM4: Nonframeshift variant in NON repetitive region in NM_020949.3.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_020949.3. 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
	SLC7A14	NM_020949.3	MANE Select	c.2304_2312delCTCTCCAGA	p.Tyr768_Glu771delinsTer	stop_gained disruptive_inframe_deletion	Exon 8 of 8	NP_066000.2	Q8TBB6
	SLC7A14-AS1	NR_135555.1		n.-226_-218delTCTGGAGAG		upstream_gene	N/A
	SLC7A14-AS1	NR_135556.1		n.-226_-218delTCTGGAGAG		upstream_gene	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC7A14	ENST00000231706.6	TSL:2 MANE Select	c.2304_2312delCTCTCCAGA	p.Tyr768_Glu771delinsTer	stop_gained disruptive_inframe_deletion	Exon 8 of 8	ENSP00000231706.4	Q8TBB6
	ENSG00000285218	ENST00000486975.1	TSL:2	c.391+43733_391+43741delCTGGAGAGT		intron	N/A	ENSP00000417434.1	B4DFI2
	ENSG00000285218	ENST00000471373.5	TSL:4	n.372+6648_372+6656delCTGGAGAGT		intron	N/A

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

ClinVar submissions

Significance: Uncertain significance

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	1	-	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		6.4

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: chr3-170184846;