1-156937288-ATG-TCT

Variant names:

• chr1-156937288-ATG-TCT
• NM_198236.3:c.4399_4401delCATinsAGA
• ARHGEF11 p.His1467Arg

Variant summary

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

The NM_198236.3(ARHGEF11):​c.4399_4401delCATinsAGA​(p.His1467Arg) 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.

• Frequency: Genomes: not found (cov: 31)
• Consequence: ARHGEF11 NM_198236.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.61
• Publications: 0 publications found

Genes affected

ARHGEF11 (HGNC:14580): (Rho guanine nucleotide exchange factor 11) Rho GTPases play a fundamental role in numerous cellular processes that are initiated by extracellular stimuli that work through G protein coupled receptors. The encoded protein may form a complex with G proteins and stimulate Rho-dependent signals. A similar protein in rat interacts with glutamate transporter EAAT4 and modulates its glutamate transport activity. Expression of the rat protein induces the reorganization of the actin cytoskeleton and its overexpression induces the formation of membrane ruffling and filopodia. Two alternative transcripts encoding different isoforms have been described. [provided by RefSeq, Jul 2008]

LRRC71 (HGNC:26556): (leucine rich repeat containing 71)

ACMG classification

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_198236.3. 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
	ARHGEF11	NM_198236.3	MANE Select	c.4399_4401delCATinsAGA	p.His1467Arg	missense	N/A	NP_937879.1	O15085-2
	ARHGEF11	NM_001377418.1		c.4390_4392delCATinsAGA	p.His1464Arg	missense	N/A	NP_001364347.1
	ARHGEF11	NM_001377419.1		c.4369_4371delCATinsAGA	p.His1457Arg	missense	N/A	NP_001364348.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ARHGEF11	ENST00000368194.8	TSL:1 MANE Select	c.4399_4401delCATinsAGA	p.His1467Arg	missense	N/A	ENSP00000357177.3	O15085-2
	ARHGEF11	ENST00000361409.2	TSL:1	c.4279_4281delCATinsAGA	p.His1427Arg	missense	N/A	ENSP00000354644.2	O15085-1
	ARHGEF11	ENST00000715594.1		c.4447_4449delCATinsAGA	p.His1483Arg	missense	N/A	ENSP00000520488.1	A0AAQ5BIK5

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		2.6

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: chr1-156907080;