21-42376583-C-A

Variant names:

• chr21-42376583-C-A
• rs727503492
• NM_001256317.3:c.1149G>T

Variant summary

Our verdict is Pathogenic. The variant received 10 ACMG points: 10P and 0B. PM1 PM2 PM5 PP2 PP3_Moderate PP5

The NM_001256317.3(TMPRSS3):​c.1149G>T​(p.Met383Ile) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,572 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. M383K) has been classified as Likely pathogenic.

• Frequency:
  • Genomes: not found (cov: 33)
  • Exomes 𝑓: 6.8e-7 (0 hom.)
• Consequence: TMPRSS3 NM_001256317.3 missense
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications P:1 U:2
• Conservation: PhyloP100: 7.24
• Publications: 1 publications found

Genes affected

TMPRSS3 (HGNC:11877): (transmembrane serine protease 3) This gene encodes a protein that belongs to the serine protease family. The encoded protein contains a serine protease domain, a transmembrane domain, an LDL receptor-like domain, and a scavenger receptor cysteine-rich domain. Serine proteases are known to be involved in a variety of biological processes, whose malfunction often leads to human diseases and disorders. This gene was identified by its association with both congenital and childhood onset autosomal recessive deafness. This gene is expressed in fetal cochlea and many other tissues, and is thought to be involved in the development and maintenance of the inner ear or the contents of the perilymph and endolymph. This gene was also identified as a tumor-associated gene that is overexpressed in ovarian tumors. Alternatively spliced transcript variants have been described. [provided by RefSeq, Jan 2012]

TMPRSS3 Gene-Disease associations (from GenCC):

• nonsyndromic genetic hearing loss

  Inheritance: AR Classification: DEFINITIVE Submitted by: ClinGen
• autosomal recessive nonsyndromic hearing loss 8

  Inheritance: AR Classification: STRONG Submitted by: PanelApp Australia, Labcorp Genetics (formerly Invitae)
• hearing loss, autosomal recessive

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Pathogenic. The variant received 10 ACMG points.

• PM1: In a hotspot region, there are 4 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 0 benign, 4 uncertain in NM_001256317.3
• PM2: Very rare variant in population databases, with high coverage
• PM5: Other missense variant is known to change same aminoacid residue: Variant chr21-42376584-A-T is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 873474.
• PP2: Missense variant in the gene, where a lot of missense mutations are associated with disease in ClinVar. The gene has 41 curated pathogenic missense variants (we use a threshold of 10). The gene has 12 curated benign missense variants. Trascript score misZ: 0.22926 (below the threshold of 3.09). GenCC associations: The gene is linked to hearing loss, autosomal recessive, autosomal recessive nonsyndromic hearing loss 8, nonsyndromic genetic hearing loss.
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.925
• PP5: Variant 21-42376583-C-A is Pathogenic according to our data. Variant chr21-42376583-C-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 165482. Variant chr21-42376583-C-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 165482. Variant chr21-42376583-C-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 165482. Variant chr21-42376583-C-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 165482. Variant chr21-42376583-C-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 165482. Variant chr21-42376583-C-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 165482. Variant chr21-42376583-C-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 165482. Variant chr21-42376583-C-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 165482. Variant chr21-42376583-C-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 165482. Variant chr21-42376583-C-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 165482. Variant chr21-42376583-C-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 165482. Variant chr21-42376583-C-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 165482. Variant chr21-42376583-C-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 165482. Variant chr21-42376583-C-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 165482. Variant chr21-42376583-C-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 165482. Variant chr21-42376583-C-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 165482. Variant chr21-42376583-C-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 165482. Variant chr21-42376583-C-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 165482. Variant chr21-42376583-C-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 165482. Variant chr21-42376583-C-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 165482.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TMPRSS3	NM_001256317.3	c.1149G>T	p.Met383Ile	missense_variant	Exon 11 of 13	ENST00000644384.2	NP_001243246.1
TMPRSS3	NM_024022.4	c.1152G>T	p.Met384Ile	missense_variant	Exon 11 of 13		NP_076927.1
TMPRSS3	NM_032404.3	c.771G>T	p.Met257Ile	missense_variant	Exon 8 of 10		NP_115780.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TMPRSS3	ENST00000644384.2	c.1149G>T	p.Met383Ile	missense_variant	Exon 11 of 13		NM_001256317.3	ENSP00000494414.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome AF: 6.84e-7 AC: 1 AN: 1461572 Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0 AN XY: 727074

African (AFR) AF: 0.00 AC: 0 AN: 33480

American (AMR) AF: 0.00 AC: 0 AN: 44724

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 26136

East Asian (EAS) AF: 0.00 AC: 0 AN: 39700

South Asian (SAS) AF: 0.00 AC: 0 AN: 86254

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 53150

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5748

European-Non Finnish (NFE) AF: 8.99e-7 AC: 1 AN: 1111992

Other (OTH) AF: 0.00 AC: 0 AN: 60388

GnomAD4 genome Cov.: 33

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Pathogenic:1 Uncertain:2

Revision: criteria provided, conflicting classifications

Submissions by phenotype

not provided Pathogenic:1

Dec 29, 2023

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This sequence change replaces methionine, which is neutral and non-polar, with isoleucine, which is neutral and non-polar, at codon 384 of the TMPRSS3 protein (p.Met384Ile). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with TMPRSS3-related conditions. ClinVar contains an entry for this variant (Variation ID: 165482). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt TMPRSS3 protein function with a positive predictive value of 95%. This variant disrupts the p.Met384 amino acid residue in TMPRSS3. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 3285355, 36633841; Invitae). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic. -

not specified Uncertain:1

May 15, 2013

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The Met384Ile variant in TMPRSS3 has not been reported in individuals with heari ng loss or in large population studies. Computational analyses (biochemical amin o acid properties, conservation, AlignGVGD, PolyPhen2, and SIFT) do not provide strong support for or against an impact to the protein. In summary, additional d ata is needed to determine the clinical significance of this variant. -

Autosomal recessive nonsyndromic hearing loss 8 Uncertain:1

Mar 09, 2015

Division of Human Genetics, Children's Hospital of Philadelphia

Significance: Uncertain significance

Review Status: no assertion criteria provided

Collection Method: research

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.96
BayesDel_addAF	Pathogenic	0.39	D
BayesDel_noAF	Pathogenic	0.33
CADD	Uncertain	24
DANN	Uncertain	1.0
DEOGEN2	Uncertain	0.73	.;D;D;.
Eigen	Uncertain	0.62
Eigen_PC	Uncertain	0.61
FATHMM_MKL	Benign	0.29	N
LIST_S2	Uncertain	0.88	D;.;D;D
M_CAP	Pathogenic	0.57	D
MetaRNN	Pathogenic	0.92	D;D;D;D
MetaSVM	Uncertain	0.50	D
MutationAssessor	Uncertain	2.3	.;M;M;.
PhyloP100		7.2
PrimateAI	Uncertain	0.61	T
PROVEAN	Uncertain	-3.8	.;.;D;D
REVEL	Pathogenic	0.81
Sift	Uncertain	0.0030	.;.;D;D
Sift4G	Uncertain	0.0090	.;.;D;D
Polyphen		0.48	P;D;D;D
Vest4		0.83, 0.83
MutPred		0.81		.;Loss of sheet (P = 0.1158);Loss of sheet (P = 0.1158);.;
MVP		0.84
MPC		0.55
ClinPred		0.99	D
GERP RS		4.9
Varity_R		0.73
gMVP		0.92
Mutation Taster		=19/81	disease causing

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

Other links and lift over

dbSNP: rs727503492; hg19: chr21-43796692;