The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]

  • See Evidence submitted by expert panel for details.

Variant: NM_194248.3(OTOF):c.2485C>T (p.Gln829Ter)

CA340525

6137 (ClinVar)

Gene: OTOF
Condition: nonsyndromic genetic deafness
Inheritance Mode: Autosomal recessive inheritance
UUID: fd96b31f-e928-4d10-85de-65170a3b6d72

HGVS expressions

NM_194248.3:c.2485C>T
NM_194248.3(OTOF):c.2485C>T (p.Gln829Ter)
NC_000002.12:g.26477210G>A
CM000664.2:g.26477210G>A
NC_000002.11:g.26700078G>A
CM000664.1:g.26700078G>A
NC_000002.10:g.26553582G>A
NG_009937.1:g.86489C>T
ENST00000272371.7:c.2485C>T
ENST00000339598.8:c.244C>T
ENST00000402415.8:c.244C>T
ENST00000272371.6:c.2485C>T
ENST00000338581.10:c.244C>T
ENST00000339598.7:c.244C>T
ENST00000402415.7:c.415C>T
ENST00000403946.7:c.2485C>T
NM_001287489.1:c.2485C>T
NM_004802.3:c.244C>T
NM_194248.2:c.2485C>T
NM_194322.2:c.415C>T
NM_194323.2:c.244C>T
NM_001287489.2:c.2485C>T
NM_004802.4:c.244C>T
NM_194322.3:c.415C>T
NM_194323.3:c.244C>T

Pathogenic

The Expert Panel has overridden the computationally generated classification - "Uncertain Significance - Insufficient Evidence"
Met criteria codes 4
PP1_Strong PM3_Very Strong PVS1 PP4
Not Met criteria codes 1
BS1

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specifications for this VCEP
Evidence submitted by expert panel
Hearing Loss VCEP
The filtering allele frequency (the lower threshold of the 95% CI of 22/34228) of the c.2485C>T (p.Gln829Ter) variant in the OTOF gene is 0.04% for Latino chromosomes in gnomAD v2.1.1, which meets the cutoff to apply BS1_Supporting. However, this variant has been established as a founder variant in the Spanish population and is thought to be causative in 3% of cases of deafness in the Spanish population (BS1_Supporting not applicable; PMID: 27177047). The p.Gln829Ter variant in OTOF is predicted to cause a premature stop codon in biologically-relevant-exon 21/46 (NM_001287489) that leads to a truncated or absent protein in a gene in which loss-of-function is an established mechanism (PVS1; PMID: 30192042). The p.Gln829Ter variant has been identified in >50 patients with non-syndromic hearing loss (PM3_VeryStrong; PMIDs: 18381613, 17036997, 16371502, 14635104, 12114484). It has repeatedly been reported to segregate with hearing loss (PP1_Strong; PMIDs: 12114484, 14635104,16371502, 18381613). In addition to hearing loss, at least 24 patients reported to have the p.Gln829Ter variant presented with features of auditory neuropathy spectrum disorder, which is highly specific to OTOF and autosomal recessive hearing loss (PP4; PMIDs:18381613, 17036997, 14635104). In summary, the p.Gln829Ter variant in OTOF meets criteria to be classified as pathogenic for autosomal recessive nonsyndromic hearing loss based on the ACMG/AMP criteria applied, as specified by the Hearing Loss Expert Panel: PVS1, PP1_Strong, PM3_VeryStrong, PP4.
Met criteria codes
PP1_Strong
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM3_Very Strong
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PVS1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PP4
auditory neuropathy observed in at least 12 patients (PMIDs: 14635104, 17036997)
Not Met criteria codes
BS1
0.04% (22/34228 CI 95%) Latino alleles in gnomAD v2.1.1, all exomes 0.016% (2/2092 CI 95%) “Other” alleles and 0.005% (3/15278 CI 95%) Latino/Admixed American alleles in gnomAD v3.1
Approved on: 2022-05-13
Published on: 2022-05-13
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