U.S. flag

An official website of the United States government

NM_005450.6(NOG):c.611G>A (p.Arg204Gln) AND multiple conditions

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
May 6, 2020
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of clinical impact:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of oncogenicity:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Record status:
current
Accession:
RCV001254352.2

Allele description [Variation Report for NM_005450.6(NOG):c.611G>A (p.Arg204Gln)]

NM_005450.6(NOG):c.611G>A (p.Arg204Gln)

Gene:
NOG:noggin [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
17q22
Genomic location:
Preferred name:
NM_005450.6(NOG):c.611G>A (p.Arg204Gln)
HGVS:
  • NC_000017.11:g.56594834G>A
  • NG_011958.1:g.6136G>A
  • NM_005450.6:c.611G>AMANE SELECT
  • NP_005441.1:p.Arg204Gln
  • NC_000017.10:g.54672195G>A
  • NM_005450.4:c.611G>A
  • p.Arg204Gln
Protein change:
R204Q
Links:
dbSNP: rs104894610
NCBI 1000 Genomes Browser:
rs104894610
Molecular consequence:
  • NM_005450.6:c.611G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Brachydactyly type B2 (BDB2)
Identifiers:
MONDO: MONDO:0012658; MedGen: C1969652; OMIM: 611377
Name:
Symphalangism-brachydactyly syndrome (SYNS1)
Synonyms:
Multiple synostoses syndrome 1; Synostoses multiple with brachydactyly; WL syndrome; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0008519; MedGen: C0342282; Orphanet: 3237; OMIM: 186500
Name:
Tarsal-carpal coalition syndrome
Identifiers:
MONDO: MONDO:0008521; MedGen: C1861305; Orphanet: 1412; OMIM: 186570
Name:
Stapes ankylosis with broad thumbs and toes
Synonyms:
ANKYLOSIS OF STAPES, HYPEROPIA, BROAD THUMBS, BROAD FIRST TOES, AND SYNDACTYLY; STAPES ANKYLOSIS SYNDROME WITHOUT SYMPHALANGISM; TEUNISSEN-CREMERS SYNDROME; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0008484; MedGen: C1866656; Orphanet: 140917; OMIM: 184460
Name:
Proximal symphalangism 1A
Identifiers:
MONDO: MONDO:0020733; MedGen: C3714899; Orphanet: 3250; OMIM: 185800

Recent activity

Clear Turn Off Turn On

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...

Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001427233Clinical Genomics Laboratory, Stanford Medicine
no assertion criteria provided
Likely pathogenic
(May 6, 2020) 		germlineclinical testing

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing

Details of each submission

From Clinical Genomics Laboratory, Stanford Medicine, SCV001427233.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providedclinical testingnot provided

Description

The p.Arg204Gln variant in the NOG gene has been previously reported in 3 related individuals from 1 family with tarsal-carpal coalition syndrome. This variant co-segregated with disease in affected family members presenting with variable skeletal anomalies including proximal symphalangism and carpal and tarsal fusion (Das Bhowmik et al., 2018). The p.Arg204Gln variant was absent from large population databases, including the Genome Aggregation Database (http://gnomad.broadinstitute.org/). Notably, a different amino acid change (p.Arg204Leu) has been previously reported at this residue, as well as amino acid changes at nearby residues (p.Leu203Pro, p.Trp205Cys), suggesting the p.Arg204Gln variant may occur in a mutational hotspot of the NOG gene. Computational tools predict that the p.Arg204Gln variant is deleterious; however, the accuracy of in silicoalgorithms is limited. These data were assessed using the ACMG/AMP variant interpretation guidelines. In summary, there is sufficient evidence to classify the p.Arg204Gln variant as likely pathogenic for a NOG-related disorder in an autosomal dominant manner based on the information above. [ACMG evidence codes used: PS2_Moderate; PM1_supporting; PM2; PP3]

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Sep 29, 2024