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NM_001368397.1(FRMPD4):c.1071-1G>A AND Intellectual disability, X-linked 104

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Apr 23, 2020
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:
RCV003985238.1

Allele description [Variation Report for NM_001368397.1(FRMPD4):c.1071-1G>A]

NM_001368397.1(FRMPD4):c.1071-1G>A

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.1071-1G>A
HGVS:
  • NC_000023.11:g.12704358G>A
  • NG_016419.3:g.886898G>A
  • NM_001368395.3:c.1182-1G>A
  • NM_001368396.3:c.1077-1G>A
  • NM_001368397.1:c.1071-1G>AMANE SELECT
  • NM_001368398.3:c.1182-1G>A
  • NM_001368399.3:c.1062-1G>A
  • NM_001368400.3:c.951-1G>A
  • NM_001368401.1:c.1047-1G>A
  • NM_001368402.3:c.1047-1G>A
  • NM_014728.3:c.1071-1G>A
  • NC_000023.10:g.12722477G>A
Molecular consequence:
  • NM_001368395.3:c.1182-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001368396.3:c.1077-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001368397.1:c.1071-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001368398.3:c.1182-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001368399.3:c.1062-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001368400.3:c.951-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001368401.1:c.1047-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001368402.3:c.1047-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_014728.3:c.1071-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]

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

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV004801609Illumina Laboratory Services, Illumina
criteria provided, single submitter

(ICSLVariantClassificationCriteria RUGD 01 April 2020)		Likely pathogenic
(Apr 23, 2020) 		unknownclinical testing

Citation Link

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Summary from all submissions

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

Details of each submission

From Illumina Laboratory Services, Illumina, SCV004801609.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

The FRMPD4 c.1071-1G>A variant results in a substitution at the consensus splice acceptor site, which is predicted to result in splicing defects that may lead to a truncated protein. A literature search was performed for the gene, cDNA change, and amino acid change. No publications were found based on this search. This variant is not observed in version 2.1.1 of the Genome Aggregation Database. This variant occurred in a de novo state in the proband. Based on the evidence, the c.1071-1G>A variant is classified as likely pathogenic for X-linked intellectual developmental disorder.

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

Last Updated: Mar 23, 2024