The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]
  • Gene label mismatch: USH2A vs undefined
  • Gene obtained from curated document aligns with the Allele Registry but not with ClinVar data
  • No CSPEC computed assertion could be determined for this classification!


Variant: NM_206933.4(USH2A):c.6233C>G (p.Pro2078Arg)

CA179550

166488 (ClinVar)

Gene: USH2A
Condition: Usher syndrome
Inheritance Mode: Autosomal recessive inheritance
UUID: 57f01c09-b6e9-4a7f-8b94-9efd6e2f985c
Approved on: 2025-01-15
Published on: 2025-03-18

HGVS expressions

NM_206933.4:c.6233C>G
NM_206933.4(USH2A):c.6233C>G
NM_206933.4(USH2A):c.6233C>G (p.Pro2078Arg)
NC_000001.11:g.216046523G>C
CM000663.2:g.216046523G>C
NC_000001.10:g.216219865G>C
CM000663.1:g.216219865G>C
NC_000001.9:g.214286488G>C
NG_009497.1:g.381874C>G
NG_009497.2:g.381926C>G
ENST00000307340.8:c.6233C>G
ENST00000674083.1:c.6233C>G
ENST00000307340.7:c.6233C>G
NM_206933.2:c.6233C>G
NM_206933.3:c.6233C>G
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Uncertain Significance

Met criteria codes 3
PM3_Supporting BS1_Supporting PP3

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specification: ClinGen Hearing Loss Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for CDH23, COCH, GJB2, KCNQ4, MYO6, MYO7A, SLC26A4, TECTA and USH2A Version 2

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Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Hearing Loss VCEP
The c.6233C>G (p.Pro2078Arg) variant in USH2A was present in 0.4% (lower bound of the 95% CI of 50/10070) of Ashkenazi Jewish alleles in gnomAD v4. However, the next highest population frequency (aside from in the "remaining" group in gnomAD) was 0.002458% (29/1179812) of non-Finnish European alleles in gnomAD v4. Because this variant is likely a founder population in the AJ population, BS1 was downgraded to BS1_Supporting. The p.Pro2078Arg variant was detected in one proband with retinitis pigmentosa and the pathogenic variant in USH2A c.12067-2A>G but phase unknown (PM3_Supporting; Hadassah-Hebrew University Medical Center internal data, ClinVar SCV001161352.1, PMID:31456290). It has also been seen in at least 8 probands without a second variant identified in USH2A (Laboratory for Molecular Medicine, Invitae internal data, GeneDx, ClinVar SCV000201902.5, SCV001068267.2, SCV005078111.1). The REVEL computational prediction tool produced a score of 0.702, which is above the threshold necessary to apply PP3. In summary, the clinical significance of this variant is uncertain. ACMG/AMP criteria applied, as specified by the Hearing Loss Expert Panel: BS1_Supporting, PM3_Supporting, PP3 (ClinGen Hearing Loss VCEP specifications version 2; 1.15.2025).
Met criteria codes
PM3_Supporting
Seen in 1 patient with RP, compound het. with c.12067-2A>G, a founder mutation that causes loss of the canonical splice acceptor site in intron 61. Phase was not determined.
BS1_Supporting
Present in 0.4965% (50/10070, 95% CI 0.39%) of Ashkenazi Jewish alleles in gnomAD v2. However, the next highest population frequencies (aside from in the "other" group in gnomAD) were 0.006% (7/113522) and 0.005% (3/64534) of non-Finnish European alleles in gnomAD v2 and v3, respectively. Because this variant is likely a founder population in the AJ population, BS1 was downgraded to BS1_Supporting.
PP3
The REVEL computational prediction tool produced a score of 0.702, which is above the threshold necessary to apply PP3.
Curation History
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