X-132084546-G-A

Variant summary

Our verdict is Likely pathogenic. Variant got 9 ACMG points: 9P and 0B. PM1PM2PP3_StrongPP5

The NM_194277.3(FRMD7):​c.685C>T​(p.Arg229Cys) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000000935 in 1,069,638 control chromosomes in the GnomAD database, with no homozygous occurrence. There are no hemizygote samples in GnomAD. In-silico tool predicts a pathogenic outcome for this variant. 12/20 in silico tools predict a damaging outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).

Frequency

Genomes: not found (cov: 23)
Exomes 𝑓: 9.3e-7 ( 0 hom. 0 hem. )

Consequence

FRMD7
NM_194277.3 missense

Scores

14
2
1

Clinical Significance

Conflicting classifications of pathogenicity criteria provided, conflicting classifications P:1U:1

Conservation

PhyloP100: 8.00
Variant links:
Genes affected
FRMD7 (HGNC:8079): (FERM domain containing 7) Predicted to enable guanyl-nucleotide exchange factor activity. Predicted to be involved in regulation of neuron projection development. Predicted to act upstream of or within several processes, including negative regulation of stress fiber assembly; positive regulation of lamellipodium assembly; and positive regulation of small GTPase mediated signal transduction. Located in cytosol; nucleoplasm; and plasma membrane. Implicated in congenital nystagmus 1. [provided by Alliance of Genome Resources, Apr 2022]

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ACMG classification

Classification made for transcript

Verdict is Likely_pathogenic. Variant got 9 ACMG points.

PM1
In a domain FERM (size 280) in uniprot entity FRMD7_HUMAN there are 14 pathogenic changes around while only 0 benign (100%) in NM_194277.3
PM2
Very rare variant in population databases, with high coverage;
PP3
MetaRNN computational evidence supports a deleterious effect, 0.977
PP5
Variant X-132084546-G-A is Pathogenic according to our data. Variant chrX-132084546-G-A is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 449483.We mark this variant Likely_pathogenic, oryginal submissions are: {Uncertain_significance=1, Pathogenic=1}.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
FRMD7NM_194277.3 linkc.685C>T p.Arg229Cys missense_variant Exon 8 of 12 ENST00000298542.9 NP_919253.1 Q6ZUT3-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
FRMD7ENST00000298542.9 linkc.685C>T p.Arg229Cys missense_variant Exon 8 of 12 1 NM_194277.3 ENSP00000298542.3 Q6ZUT3-1
FRMD7ENST00000464296.1 linkc.640C>T p.Arg214Cys missense_variant Exon 8 of 12 1 ENSP00000417996.1 Q6ZUT3-2
FRMD7ENST00000370879.5 linkc.325C>T p.Arg109Cys missense_variant Exon 4 of 8 1 ENSP00000359916.1 X6R7S7

Frequencies

GnomAD3 genomes
Cov.:
23
GnomAD4 exome
AF:
9.35e-7
AC:
1
AN:
1069638
Hom.:
0
Cov.:
25
AF XY:
0.00
AC XY:
0
AN XY:
338944
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000123
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
23

ClinVar

Significance: Conflicting classifications of pathogenicity
Submissions summary: Pathogenic:1Uncertain:1
Revision: criteria provided, conflicting classifications
LINK: link

Submissions by phenotype

not provided Pathogenic:1Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpMar 01, 2022In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. This sequence change replaces arginine, which is basic and polar, with cysteine, which is neutral and slightly polar, at codon 229 of the FRMD7 protein (p.Arg229Cys). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individual(s) with congenital motor nystagmus (PMID: 17768376, 28623544). ClinVar contains an entry for this variant (Variation ID: 449483). Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be disruptive. Experimental studies have shown that this missense change affects FRMD7 function (PMID: 23406872). This variant disrupts the p.Arg229 amino acid residue in FRMD7. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 17962394). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. -
Pathogenic, criteria provided, single submitterclinical testingGeneDxJul 10, 2021Published functional studies demonstrate a damaging effect with reduced R229C mutant protein expression, as compared to wild-type, and dominant-negative inhibition of neurite outgrowth (Watkins et al., 2013); Not observed at significant frequency in large population cohorts (Lek et al., 2016); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 17768376, 23406872, 28623544, 19072571, 27535533, 21904664) -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
0.75
BayesDel_addAF
Pathogenic
0.59
D
BayesDel_noAF
Pathogenic
0.60
CADD
Pathogenic
29
DANN
Pathogenic
1.0
DEOGEN2
Uncertain
0.73
.;D;.
FATHMM_MKL
Pathogenic
0.98
D
LIST_S2
Pathogenic
1.0
D;D;D
M_CAP
Pathogenic
0.77
D
MetaRNN
Pathogenic
0.98
D;D;D
MetaSVM
Pathogenic
0.83
D
MutationAssessor
Pathogenic
3.3
.;M;.
PrimateAI
Pathogenic
0.89
D
PROVEAN
Pathogenic
-6.9
D;D;D
REVEL
Pathogenic
0.86
Sift
Uncertain
0.0010
D;D;D
Sift4G
Pathogenic
0.0010
D;D;D
Polyphen
1.0
.;D;D
Vest4
0.87
MutPred
0.89
.;Gain of methylation at K230 (P = 0.037);.;
MVP
0.99
MPC
1.0
ClinPred
1.0
D
GERP RS
5.9
Varity_R
0.91
gMVP
0.79

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs137852212; hg19: chrX-131218574; COSMIC: COSV53747620; API