rs116840789

chr3-8745547-G-Achr3-8745547-G-T

Variant summary

Our verdict is Pathogenic. Variant got 16 ACMG points: 16P and 0B. PM1 PM5 PP3_Strong PP5_Very_Strong

The NM_033337.3(CAV3):c.136G>A(p.Ala46Thr) variant causes a missense change involving the alteration of a conserved nucleotide. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A46E) has been classified as Uncertain significance.

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: CAV3 NM_033337.3 missense
• Clinical Significance: Pathogenic criteria provided, multiple submitters, no conflicts P:8 O:1
• Conservation: PhyloP100: 9.52

Genes affected

CAV3 (HGNC:1529): (caveolin 3) This gene encodes a caveolin family member, which functions as a component of the caveolae plasma membranes found in most cell types. Caveolin proteins are proposed to be scaffolding proteins for organizing and concentrating certain caveolin-interacting molecules. Mutations identified in this gene lead to interference with protein oligomerization or intra-cellular routing, disrupting caveolae formation and resulting in Limb-Girdle muscular dystrophy type-1C (LGMD-1C), hyperCKemia or rippling muscle disease (RMD). Alternative splicing has been identified for this locus, with inclusion or exclusion of a differentially spliced intron. In addition, transcripts utilize multiple polyA sites and contain two potential translation initiation sites. [provided by RefSeq, Jul 2008]

OXTR (HGNC:):

ACMG classification

Verdict is Pathogenic. Variant got 16 ACMG points.

• PM1: In a topological_domain Cytoplasmic (size 82) in uniprot entity CAV3_HUMAN there are 61 pathogenic changes around while only 13 benign (82%) in NM_033337.3
• PM5: Other missense variant is known to change same aminoacid residue: Variant chr3-8745548-C-T is described in ClinVar as [Likely_pathogenic]. Clinvar id is 8282.Status of the report is criteria_provided_single_submitter, 1 stars.
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.995
• PP5: Variant 3-8745547-G-A is Pathogenic according to our data. Variant chr3-8745547-G-A is described in ClinVar as [Pathogenic]. Clinvar id is 8281.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-8745547-G-A is described in Lovd as [Pathogenic]. Variant chr3-8745547-G-A is described in Lovd as [Pathogenic]. Variant chr3-8745547-G-A is described in Lovd as [Likely_pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CAV3	NM_033337.3	c.136G>A	p.Ala46Thr	missense_variant	2/2	ENST00000343849.3
CAV3	NM_001234.5	c.136G>A	p.Ala46Thr	missense_variant	2/3
OXTR	XR_007095681.1	n.1885-2945C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CAV3	ENST00000343849.3	c.136G>A	p.Ala46Thr	missense_variant	2/2	1	NM_033337.3	P1
CAV3	ENST00000397368.2	c.136G>A	p.Ala46Thr	missense_variant	2/3	1		P1
CAV3	ENST00000472766.1	n.155+11557G>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 1461776 Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0 AN XY: 727184

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: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 32

Alfa AF: 0.0000454 Hom.: 0

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:8 Other:1

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Pathogenic:4 Other:1

Pathogenic, criteria provided, single submitter	clinical testing	Athena Diagnostics	Sep 07, 2016	- -
Pathogenic, criteria provided, single submitter	clinical testing	Eurofins Ntd Llc (ga)	Jan 06, 2017	- -
not provided, no classification provided	curation	Leiden Muscular Dystrophy (CAV3)	Apr 15, 2012	- -
Pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Aug 31, 2022	Published functional studies demonstrate a damaging effect (Brauers et al., 2010); Not observed at significant frequency in large population cohorts (gnomAD); 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: 15580566, 20229577, 11431690, 31862442, 20472890, 22976939, 21660982, 18583131, 11001938, 26947586, 28807458, 33963534, 32528171, 25630502, 17994539) -
Pathogenic, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Feb 01, 2020	- -

Elevated circulating creatine kinase concentration Pathogenic:1

Pathogenic, no assertion criteria provided

literature only

OMIM

Jan 01, 2005

- -

Long QT syndrome Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Invitae

Oct 06, 2023

This sequence change replaces alanine, which is neutral and non-polar, with threonine, which is neutral and polar, at codon 46 of the CAV3 protein (p.Ala46Thr). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individual(s) with caveolinopathies (PMID: 11001938, 11431690, 15580566, 18583131, 20229577, 21660982, 22976939, 26947586). In at least one individual the variant was observed to be de novo. It has also been observed to segregate with disease in related individuals. This variant is also known as p.Ala45Thr. ClinVar contains an entry for this variant (Variation ID: 8281). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be disruptive. Experimental studies have shown that this missense change affects CAV3 function (PMID: 11431690, 20472890). For these reasons, this variant has been classified as Pathogenic. -

Rippling muscle disease 2 Pathogenic:1

Pathogenic, no assertion criteria provided

literature only

OMIM

Jan 01, 2005

- -

Cardiovascular phenotype Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Ambry Genetics

Feb 19, 2021

The p.A46T pathogenic mutation (also known as p.A45T and c.136G>A), located in coding exon 2 of the CAV3 gene, results from a G to A substitution at nucleotide position 136. The alanine at codon 46 is replaced by threonine, an amino acid with similar properties. This mutation has been reported in individuals with a range of caveolinopathies, including limb girdle muscular dystrophy type 1C, rippling muscle disease, hyperCKemia, and asymmetric distal myopathy (Fulizio L et al. Hum Mutat, 2005 Jan;25:82-9; Guglieri M et al. Hum Mutat, 2008 Feb;29:258-66; Aboumousa A et al. Neuromuscul Disord, 2008 Jul;18:572-8; Harris E et al. Orphanet J Rare Dis, 2017 09;12:151). This variant also showed segregation with affected phenotypes across multiple generations in a large Swedish family (Sundblom J et al. Muscle Nerve, 2010 Jun;41:751-7). In addition, at least three reportedly de novo cases with absent or reduced CAV3 expression have been documented (Herrmann R et al. Hum Mol Genet, 2000 Sep;9:2335-40; Arias Gómez M et al. Muscle Nerve, 2011 Jul;44:126-8; Chen J et al. Neuropathology, 2016 Oct;36:485-489). Limited functional studies also demonstrated lower CAV3 surface expression (Brauers E et al. Am J Pathol, 2010 Jul;177:261-70). Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.96
BayesDel_addAF	Pathogenic	0.56	D
BayesDel_noAF	Pathogenic	0.57
Cadd	Pathogenic	30
Dann	Uncertain	1.0
DEOGEN2	Pathogenic	0.97	D;D
Eigen	Pathogenic	0.76
Eigen_PC	Uncertain	0.62
FATHMM_MKL	Pathogenic	0.99	D
M_CAP	Pathogenic	0.44	D
MetaRNN	Pathogenic	0.99	D;D
MetaSVM	Pathogenic	1.1	D
MutationAssessor	Pathogenic	3.6	H;H
MutationTaster	Benign	1.0	D;D
PrimateAI	Uncertain	0.71	T
PROVEAN	Uncertain	-3.9	D;D
REVEL	Pathogenic	0.92
Sift	Uncertain	0.0010	D;D
Sift4G	Pathogenic	0.0	D;D
Polyphen		1.0	D;D
Vest4		0.93
MutPred		0.93		Gain of glycosylation at A46 (P = 0.043);Gain of glycosylation at A46 (P = 0.043);
MVP		1.0
MPC		1.4
ClinPred		1.0	D
GERP RS		4.8
Varity_R		0.94
gMVP		0.92

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs116840789; hg19: chr3-8787233; COSMIC: COSV57481483; COSMIC: COSV57481483;