11-121109339-C-T

Variant names:

• chr11-121109339-C-T
• rs727504830
• NM_005422.4:c.327C>T

Variant summary

Our verdict is Uncertain significance. The variant received 1 ACMG points: 2P and 1B. PP3 PP5 BS1_Supporting

The NM_005422.4(TECTA):​c.327C>T​(p.Gly109Gly) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000378 in 1,613,988 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).

• Frequency:
  • Genomes: 𝑓 0.00024 (0 hom., cov: 32)
  • Exomes 𝑓: 0.000017 (0 hom.)
• Consequence: TECTA NM_005422.4 synonymous
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications P:4 U:3
• Conservation: PhyloP100: -0.382
• Publications: 1 publications found

Genes affected

TECTA (HGNC:11720): (tectorin alpha) The tectorial membrane is an extracellular matrix of the inner ear that contacts the stereocilia bundles of specialized sensory hair cells. Sound induces movement of these hair cells relative to the tectorial membrane, deflects the stereocilia, and leads to fluctuations in hair-cell membrane potential, transducing sound into electrical signals. Alpha-tectorin is one of the major noncollagenous components of the tectorial membrane. Mutations in the TECTA gene have been shown to be responsible for autosomal dominant nonsyndromic hearing impairment and a recessive form of sensorineural pre-lingual non-syndromic deafness. [provided by RefSeq, Jul 2008]

TBCEL-TECTA (HGNC:54857): (TBCEL-TECTA readthrough) Predicted to enable alpha-tubulin binding activity. Predicted to be involved in microtubule cytoskeleton organization; post-chaperonin tubulin folding pathway; and tubulin complex assembly. Predicted to be active in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Uncertain_significance. The variant received 1 ACMG points.

• PP3: Splicing predictors support a deleterious effect. Scorers claiming Pathogenic: max_spliceai. No scorers claiming Uncertain. No scorers claiming Benign.
• PP5: Variant 11-121109339-C-T is Pathogenic according to our data. Variant chr11-121109339-C-T is described in ClinVar as Conflicting_classifications_of_pathogenicity. ClinVar VariationId is 179381.
• BS1: Variant frequency is greater than expected in population amr. GnomAd4 allele frequency = 0.000237 (36/152108) while in subpopulation AMR AF = 0.00216 (33/15272). AF 95% confidence interval is 0.00158. There are 0 homozygotes in GnomAd4. There are 19 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check. Existence of Clinvar submissions makes me limit the strength of this signal to Supporting

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_005422.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TECTA	NM_005422.4	MANE Select	c.327C>T	p.Gly109Gly	synonymous	Exon 4 of 24	NP_005413.2
	TBCEL-TECTA	NM_001378761.1		c.1284C>T	p.Gly428Gly	synonymous	Exon 10 of 30	NP_001365690.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TECTA	ENST00000392793.6	TSL:5 MANE Select	c.327C>T	p.Gly109Gly	synonymous	Exon 4 of 24	ENSP00000376543.1
	TECTA	ENST00000264037.2	TSL:1	c.327C>T	p.Gly109Gly	synonymous	Exon 3 of 23	ENSP00000264037.2
	TBCEL-TECTA	ENST00000645041.1		c.1236C>T	p.Gly412Gly	synonymous	Exon 9 of 10	ENSP00000496315.1

Frequencies

GnomAD3 genomes AF: 0.000237 AC: 36 AN: 152108 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.0000242

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00216

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000294

Gnomad OTH AF: 0.00

GnomAD2 exomes AF: 0.0000159 AC: 4 AN: 251416 AF XY: 0.0000221

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00000879

Gnomad OTH exome AF: 0.000489

GnomAD4 exome AF: 0.0000171 AC: 25 AN: 1461880 Hom.: 0 Cov.: 31 AF XY: 0.0000151 AC XY: 11 AN XY: 727240

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

American (AMR) AF: 0.000268 AC: 12 AN: 44724

Ashkenazi Jewish (ASJ) AF: 0.0000383 AC: 1 AN: 26136

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

South Asian (SAS) AF: 0.00 AC: 0 AN: 86256

European-Finnish (FIN) AF: 0.0000187 AC: 1 AN: 53416

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5768

European-Non Finnish (NFE) AF: 0.00000180 AC: 2 AN: 1112004

Other (OTH) AF: 0.000149 AC: 9 AN: 60396

GnomAD4 genome AF: 0.000237 AC: 36 AN: 152108 Hom.: 0 Cov.: 32 AF XY: 0.000256 AC XY: 19 AN XY: 74290

African (AFR) AF: 0.0000242 AC: 1 AN: 41406

American (AMR) AF: 0.00216 AC: 33 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3472

East Asian (EAS) AF: 0.00 AC: 0 AN: 5190

South Asian (SAS) AF: 0.00 AC: 0 AN: 4820

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10596

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 316

European-Non Finnish (NFE) AF: 0.0000294 AC: 2 AN: 68030

Other (OTH) AF: 0.00 AC: 0 AN: 2094

Alfa AF: 0.0000434 Hom.: 0

Bravo AF: 0.000468

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Pathogenic:4 Uncertain:3

Revision: criteria provided, conflicting classifications

Submissions by phenotype

not provided Pathogenic:2 Uncertain:2

May 05, 2017

Eurofins Ntd Llc (ga)

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Jan 29, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This sequence change affects codon 109 of the TECTA mRNA. It is a 'silent' change, meaning that it does not change the encoded amino acid sequence of the TECTA protein. This variant is present in population databases (rs727504830, gnomAD 0.003%). This variant has been observed in individual(s) with autosomal recessive deafness (PMID: 35870179; internal data). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 179381). Studies have shown that this variant alters mRNA splicing and is expected to lead to the loss of protein expression (PMID: 35870179). For these reasons, this variant has been classified as Pathogenic.

Sep 06, 2024

GeneDx

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Published functional studies suggest a damaging effect on gene splicing due to activation of a cryptic splice donor site (PMID: 35870179); Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports a deleterious effect on splicing; This variant is associated with the following publications: (PMID: 35870179)

Jul 31, 2018

Athena Diagnostics

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Autosomal recessive nonsyndromic hearing loss 21 Pathogenic:1

Jun 30, 2025

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Variant summary: TECTA c.327C>T alters a conserved nucleotide resulting in a synonymous change. Several computational tools predict a significant impact on normal splicing: Four predict the variant creates a 5' donor site. At least one publication reports experimental evidence that this variant affects mRNA splicing (Chen_2022). The variant allele was found at a frequency of 1.6e-05 in 251416 control chromosomes. c.327C>T has been observed in multiple individuals affected with Deafness, Autosomal Recessive 21 (Chen_2022) and observed to segregate with disease. These data indicate that the variant is very likely to be associated with disease. The following publication have been ascertained in the context of this evaluation (PMID: 35870179). ClinVar contains an entry for this variant (Variation ID: 179381). Based on the evidence outlined above, the variant was classified as pathogenic.

TECTA-related disorder Pathogenic:1

Apr 24, 2024

PreventionGenetics, part of Exact Sciences

Significance: Likely pathogenic

Review Status: no assertion criteria provided

Collection Method: clinical testing

The TECTA c.327C>T variant is not predicted to result in an amino acid change (p.=). This variant has been reported in the homozygous and compound heterozygous states in multiple unrelated individuals with nonsyndromic hearing loss, with an in vitro splicing assay demonstrating this variant results in the creation of a cryptic splice donor site, frameshift and premature termination (Chen. 2022. PubMed ID: 35870179). This variant is reported in 0.00088% of alleles in individuals of European (Non-Finnish) descent in gnomAD. This variant is interpreted as likely pathogenic.

not specified Uncertain:1

Jul 27, 2018

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Variant classified as Uncertain Significance - Favor Pathogenic. The p.Gly109Gly variant in TECTA has been reported by our laboratory in three individuals with hearing loss, including this case. In one family, the proband was compound heter ozygous for a second variant of uncertain significance in TECTA; however, the p. Gly109Gly variant did not segregate in the individual's affected sibling and the refore TECTA was ruled out as a cause of hearing loss. In the second family, the proband carried a pathogenic variant in TECTA that was likely in trans, as one parent was tested for the two variants but only harbored one. In a third family (this case), the variant is identified in homozygosity. This variant has also b een reported as a VUS in ClinVar (Variation ID# 179381). It has also been ident ified in 1/33580 Latino chromosomes by the Genome Aggregation Database (gnomAD, http://gnomad.broadinstitute.org). While the variant does not alter an amino aci d residue, computational tools suggest the creation of a cryptic splice site. Ho wever, this information is not predictive enough to determine pathogenicity. In summary, the clinical significance of the p.Gly109Gly variant is uncertain but w e would lean towards a more likely pathogenic role. ACMG/AMP criteria applied: P M2, PM3, PP3.

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.37
CADD	Benign	18
DANN	Benign	0.53
PhyloP100		-0.38

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.51		Details are displayed if max score is > 0.2
DS_DG_spliceai		0.51		Position offset: -2

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

Other links and lift over

dbSNP: rs727504830; hg19: chr11-120980048; COSMIC: COSV99881675;