1-161000194-AC-GT

Variant names:

• chr1-161000194-AC-GT
• NM_016946.6:c.542_543delGTinsAC
• F11R p.Arg181His

Variant summary

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

The NM_016946.6(F11R):​c.542_543delGTinsAC​(p.Arg181His) 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 variant affecting the same amino acid position, but resulting in a different missense (i.e. R181L) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 31)
• Consequence: F11R NM_016946.6 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.52
• Publications: 0 publications found

Genes affected

F11R (HGNC:14685): (F11 receptor) Tight junctions represent one mode of cell-to-cell adhesion in epithelial or endothelial cell sheets, forming continuous seals around cells and serving as a physical barrier to prevent solutes and water from passing freely through the paracellular space. The protein encoded by this immunoglobulin superfamily gene member is an important regulator of tight junction assembly in epithelia. In addition, the encoded protein can act as (1) a receptor for reovirus, (2) a ligand for the integrin LFA1, involved in leukocyte transmigration, and (3) a platelet receptor. Multiple 5' alternatively spliced variants, encoding the same protein, have been identified but their biological validity has not been established. [provided by RefSeq, Jul 2008]

ENSG00000270149 (HGNC:):

ACMG classification

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_016946.6. 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
	F11R	NM_016946.6	MANE Select	c.542_543delGTinsAC	p.Arg181His	missense	N/A	NP_058642.1	Q6FIB4
	F11R	NM_001382727.1		c.542_543delGTinsAC	p.Arg181His	missense	N/A	NP_001369656.1
	F11R	NM_001382730.1		c.542_543delGTinsAC	p.Arg181His	missense	N/A	NP_001369659.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	F11R	ENST00000368026.11	TSL:1 MANE Select	c.542_543delGTinsAC	p.Arg181His	missense	N/A	ENSP00000357005.5	Q9Y624-1
	ENSG00000270149	ENST00000289779.7	TSL:2	n.*583_*584delGTinsAC		non_coding_transcript_exon	Exon 8 of 13	ENSP00000289779.4	A0A0A0MQY5
	ENSG00000270149	ENST00000289779.7	TSL:2	n.*583_*584delGTinsAC		3_prime_UTR	Exon 8 of 13	ENSP00000289779.4	A0A0A0MQY5

Frequencies

GnomAD3 genomes Cov.: 31

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

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		1.5

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: chr1-160969984;