rs1060500720

Variant names:

• chrX-154349458-G-T
• rs1060500720
• NM_001110556.2:c.7660C>A

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_001110556.2(FLNA):​c.7660C>A​(p.Pro2554Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 26)
• Consequence: FLNA NM_001110556.2 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: -0.349

Genes affected

FLNA (HGNC:3754): (filamin A) The protein encoded by this gene is an actin-binding protein that crosslinks actin filaments and links actin filaments to membrane glycoproteins. The encoded protein is involved in remodeling the cytoskeleton to effect changes in cell shape and migration. This protein interacts with integrins, transmembrane receptor complexes, and second messengers. Defects in this gene are a cause of several syndromes, including periventricular nodular heterotopias (PVNH1, PVNH4), otopalatodigital syndromes (OPD1, OPD2), frontometaphyseal dysplasia (FMD), Melnick-Needles syndrome (MNS), and X-linked congenital idiopathic intestinal pseudoobstruction (CIIPX). Two transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Mar 2009]

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.072612554).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FLNA	NM_001110556.2	c.7660C>A	p.Pro2554Thr	missense_variant	Exon 47 of 48	ENST00000369850.10	NP_001104026.1
FLNA	NM_001456.4	c.7636C>A	p.Pro2546Thr	missense_variant	Exon 46 of 47		NP_001447.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FLNA	ENST00000369850.10	c.7660C>A	p.Pro2554Thr	missense_variant	Exon 47 of 48	1	NM_001110556.2	ENSP00000358866.3

Frequencies

GnomAD3 genomes Cov.: 26

GnomAD4 exome Cov.: 33

GnomAD4 genome Cov.: 26

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

Melnick-Needles syndrome;C0265293:Frontometaphyseal dysplasia;C1844696:Oto-palato-digital syndrome, type II;C1848213:Heterotopia, periventricular, X-linked dominant Uncertain:1

Dec 18, 2020

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This sequence change replaces proline with threonine at codon 2546 of the FLNA protein (p.Pro2546Thr). The proline residue is weakly conserved and there is a small physicochemical difference between proline and threonine. This variant is not present in population databases (ExAC no frequency) and has not been reported in the literature in individuals with a FLNA-related disease. In summary, this variant is a novel missense change that is not predicted to affect protein function. There is no indication that it causes disease, but the available evidence is currently insufficient to prove that conclusively. Therefore, it has been classified as a Variant of Uncertain Significance. 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 tolerated, but these predictions have not been confirmed by published functional studies. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.057
BayesDel_addAF	Benign	-0.24	T
BayesDel_noAF	Benign	-0.59
CADD	Benign	6.6
DANN	Benign	0.60
DEOGEN2	Benign	0.27	T;.;.;.;.
FATHMM_MKL	Benign	0.71	D
LIST_S2	Benign	0.39	T;T;.;T;T
M_CAP	Benign	0.030	D
MetaRNN	Benign	0.073	T;T;T;T;T
MetaSVM	Benign	-0.92	T
MutationAssessor	Benign	0.46	N;.;.;.;.
PrimateAI	Benign	0.40	T
PROVEAN	Benign	1.4	N;.;N;N;.
REVEL	Benign	0.18
Sift	Benign	0.61	T;.;T;T;.
Sift4G	Benign	0.60	T;T;T;T;T
Polyphen		0.0030	B;.;B;B;.
Vest4		0.076
MutPred		0.38		Gain of phosphorylation at P2554 (P = 0.0188);.;.;.;.;
MVP		0.63
MPC		0.57
ClinPred		0.079	T
GERP RS		-0.25
Varity_R		0.056
gMVP		0.32

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.060		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

Other links and lift over

dbSNP: rs1060500720; hg19: chrX-153577826;