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NM_001368397.1(FRMPD4):c.2161G>A (p.Asp721Asn) AND Intellectual disability, X-linked 104

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Jul 16, 2021
Review status:
1 star out of maximum of 4 stars
criteria provided, single submitter
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:
RCV002266696.1

Allele description [Variation Report for NM_001368397.1(FRMPD4):c.2161G>A (p.Asp721Asn)]

NM_001368397.1(FRMPD4):c.2161G>A (p.Asp721Asn)

Gene:
FRMPD4:FERM and PDZ domain containing 4 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
Xp22.2
Genomic location:
Preferred name:
NM_001368397.1(FRMPD4):c.2161G>A (p.Asp721Asn)
HGVS:
  • NC_000023.11:g.12716620G>A
  • NG_016419.3:g.899160G>A
  • NM_001368395.3:c.2272G>A
  • NM_001368396.3:c.2167G>A
  • NM_001368397.1:c.2161G>AMANE SELECT
  • NM_001368398.3:c.2272G>A
  • NM_001368399.3:c.2152G>A
  • NM_001368400.3:c.2041G>A
  • NM_001368401.1:c.2137G>A
  • NM_001368402.3:c.2137G>A
  • NM_014728.3:c.2161G>A
  • NP_001355324.1:p.Asp758Asn
  • NP_001355325.1:p.Asp723Asn
  • NP_001355326.1:p.Asp721Asn
  • NP_001355327.1:p.Asp758Asn
  • NP_001355328.1:p.Asp718Asn
  • NP_001355329.1:p.Asp681Asn
  • NP_001355330.1:p.Asp713Asn
  • NP_001355331.1:p.Asp713Asn
  • NP_055543.2:p.Asp721Asn
  • NC_000023.10:g.12734739G>A
Protein change:
D681N
Links:
dbSNP: rs147167664
NCBI 1000 Genomes Browser:
rs147167664
Molecular consequence:
  • NM_001368395.3:c.2272G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001368396.3:c.2167G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001368397.1:c.2161G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001368398.3:c.2272G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001368399.3:c.2152G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001368400.3:c.2041G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001368401.1:c.2137G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001368402.3:c.2137G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_014728.3:c.2161G>A - missense variant - [Sequence Ontology: SO:0001583]
Observations:
1

Condition(s)

Name:
Intellectual disability, X-linked 104 (XLID104)
Synonyms:
INTELLECTUAL DEVELOPMENTAL DISORDER, X-LINKED 104
Identifiers:
MONDO: MONDO:0010509; MedGen: C4310817; OMIM: 300983

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV002548767New York Genome Center - CSER-NYCKidSeq
criteria provided, single submitter

(NYGC Assertion Criteria 2020)
Uncertain significance
(Jul 16, 2021)
inheritedclinical testing

Citation Link

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedinheritedunknown1not providednot provided1not providedclinical testing

Details of each submission

From New York Genome Center - CSER-NYCKidSeq, SCV002548767.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testingnot provided

Description

The inherited c.2161G>A, p.Asp721Asn variant identified in the FRMPD4 gene has not been reported in the literature in individuals with FRMPD4-related conditions. This variant has four heterozygous alleles in gnomAD v3.1.1 suggesting it is not a common benign variant in the populations represented in this database. In silico algorithms predict a conflicting interpretation of pathogenicity. Given the lack of compelling evidence for its pathogenicity, the inherited c.2161G>A, p.Asp721Asn variant identified in the FRMPD4 gene is reported as a Variant of Uncertain Significance.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1inheritedunknown1not providednot provided1not providednot providednot provided

Last Updated: Dec 24, 2023