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


Variant: NM_194248.3(OTOF):c.5374C>T (p.Arg1792Cys)

CA182451

178503 (ClinVar)

Gene: OTOF
Condition: nonsyndromic genetic deafness
Inheritance Mode: Autosomal recessive inheritance
UUID: 71c2ce3c-1d30-4ad1-b66d-cee7e0ffa15c
Approved on: 2023-06-29
Published on: 2023-06-30

HGVS expressions

NM_194248.3:c.5374C>T
NM_194248.3(OTOF):c.5374C>T (p.Arg1792Cys)
NC_000002.12:g.26461855G>A
CM000664.2:g.26461855G>A
NC_000002.11:g.26684723G>A
CM000664.1:g.26684723G>A
NC_000002.10:g.26538227G>A
NG_009937.1:g.101844C>T
ENST00000272371.7:c.5374C>T
ENST00000339598.8:c.3073C>T
ENST00000402415.8:c.3133C>T
ENST00000272371.6:c.5374C>T
ENST00000338581.10:c.3073C>T
ENST00000339598.7:c.3073C>T
ENST00000402415.7:c.3304C>T
ENST00000403946.7:c.5374C>T
NM_001287489.1:c.5374C>T
NM_004802.3:c.3073C>T
NM_194248.2:c.5374C>T
NM_194322.2:c.3304C>T
NM_194323.2:c.3073C>T
NM_001287489.2:c.5374C>T
NM_004802.4:c.3073C>T
NM_194322.3:c.3304C>T
NM_194323.3:c.3073C>T
More

Likely Pathogenic

Met criteria codes 5
PP4 PP3 PM3 PM5 PM2_Supporting
Not Met criteria codes 18
PS4 PS3 PS2 PS1 BP7 BP5 BP3 BP2 BP4 PP1 PVS1 PM6 PM4 PM1 BA1 BS2 BS4 BS1

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specification: ClinGen Hearing Loss Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for OTOF and MYO15A Version 1

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Hearing Loss VCEP
The c.5374C>T variant in OTOF is a missense variant predicted to cause substitution of arginine by cysteine at amino acid 1792. The highest population minor allele frequency in gnomAD v2.1.1 is 0.00006152 (1/16256 alleles) in the African/African American population, which is lower than the ClinGen Hearing Loss VCEP threshold (<0.00007) for PM2_Supporting, meeting this criterion (PM2_Supporting). The computational predictor REVEL gives a score of 0.843, which is above the threshold of 0.7, evidence that correlates with impact to OTOF function (PP3). 1 different missense variant, c.5375G>A (p.R1792H) (PMID: 29048421, ClinVar Variation ID: 48259), in the same codon has been classified as likely pathogenic for nonsyndromic hearing loss by multiple submitters in ClinVar (PM5). This variant has been detected in at least 3 individuals with AR deafness. For two of those individuals, both were compound heterozygous for the variant and a VUS meeting PM2_Supporting, and both of those were confirmed in trans by family testing (c.2676G>A (p.K892K) which occurs at the last nucleotide in exon (22) of OTOF and c.4748G>A (p.R1583H), 1.5 PM3 points, PMID: 34416374, Universitätsmedizin Göttingen, Institute of Human Genetics/Institute of Auditory Neuroscience & InnerEarLab) (PM3). ​​At least one patient was compound heterozygous for this variant and the p.K892K variant displayed auditory neuropathy spectrum disorder (ANSD), which is highly specific for autosomal recessive deafness (PP4, PMID: 34416374). In summary, this variant meets the criteria to be classified as likely pathogenic for autosomal recessive nonsyndromic hearing loss based on the ACMG/AMP criteria applied, as specified by the ClinGen Hearing Loss VCEP: PM2_P, PP3, PP4, PM3, PM5 (ClinGen Hearing Loss VCEP specifications version 2; 6/27/2022).
Met criteria codes
PP4
At least one patient was compound heterozygous for this variant and the p.K892K variant displayed auditory neuropathy spectrum disorder (ANSD), which is highly specific for autosomal recessive deafness (PP4, PMID: 34416374).
PP3
The computational predictor REVEL gives a score of 0.843, which is above the threshold of 0.7, evidence that correlates with impact to OTOF function (PP3).
PM3
This variant has been detected in at least 3 individuals with AR deafness. For two of those individuals, both were compound heterozygous for the variant and a VUS meeting PM2_Supporting, and both of those were confirmed in trans by family testing (c.2676G>A (p.K892K) which occurs at the last nucleotide in exon (22) of OTOF and c.4748G>A (p.R1583H), 1.5 PM3 points, PMID: 34416374, Universitätsmedizin Göttingen, Institute of Human Genetics/Institute of Auditory Neuroscience & InnerEarLab) (PM3).
PM5
1 different missense variant, c.5375G>A (p.R1792H) (PMID: 29048421, ClinVar Variation ID: 48259), in the same codon has been classified as likely pathogenic for nonsyndromic hearing loss by multiple submitters in ClinVar (PM5).
PM2_Supporting
The highest population minor allele frequency in gnomAD v2.1.1 is 0.00006152 (1/16256 alleles) in the African/African American population, which is lower than the ClinGen Hearing Loss VCEP threshold (<0.00007) for PM2_Supporting, meeting this criterion (PM2_Supporting).
Not Met criteria codes
PS4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP7
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP5
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PP1
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
PM6
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BA1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BS2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BS4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BS1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
Curation History
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