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NM_001352027.3(PHF21A):c.1741C>T (p.Arg581Ter) AND Intellectual disability

Germline classification:
Likely pathogenic (2 submissions)
Last evaluated:
Apr 20, 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:
RCV000760234.8

Allele description [Variation Report for NM_001352027.3(PHF21A):c.1741C>T (p.Arg581Ter)]

NM_001352027.3(PHF21A):c.1741C>T (p.Arg581Ter)

Gene:
PHF21A:PHD finger protein 21A [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
11p11.2
Genomic location:
Preferred name:
NM_001352027.3(PHF21A):c.1741C>T (p.Arg581Ter)
HGVS:
  • NC_000011.10:g.45935683G>A
  • NM_001101802.3:c.1738C>T
  • NM_001352025.3:c.1741C>T
  • NM_001352026.3:c.1741C>T
  • NM_001352027.3:c.1741C>TMANE SELECT
  • NM_001352028.1:c.1600C>T
  • NM_001352029.1:c.1600C>T
  • NM_001352030.3:c.1597C>T
  • NM_001352031.3:c.1597C>T
  • NM_001352032.3:c.1597C>T
  • NM_016621.5:c.1600C>T
  • NP_001095272.1:p.Arg580Ter
  • NP_001338954.1:p.Arg581Ter
  • NP_001338955.1:p.Arg581Ter
  • NP_001338956.1:p.Arg581Ter
  • NP_001338957.1:p.Arg534Ter
  • NP_001338958.1:p.Arg534Ter
  • NP_001338959.1:p.Arg533Ter
  • NP_001338960.1:p.Arg533Ter
  • NP_001338961.1:p.Arg533Ter
  • NP_057705.3:p.Arg534Ter
  • NC_000011.9:g.45957234G>A
  • NM_001101802.1:c.1738C>T
  • NM_016621.3:c.1600C>T
  • NR_147890.3:n.2244C>T
  • NR_165446.1:n.2480C>T
Protein change:
R533*; ARG580TER
Links:
OMIM: 608325.0002
Molecular consequence:
  • NR_147890.3:n.2244C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_165446.1:n.2480C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NM_001101802.3:c.1738C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001352025.3:c.1741C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001352026.3:c.1741C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001352027.3:c.1741C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001352028.1:c.1600C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001352029.1:c.1600C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001352030.3:c.1597C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001352031.3:c.1597C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001352032.3:c.1597C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_016621.5:c.1600C>T - nonsense - [Sequence Ontology: SO:0001587]
Observations:
1

Condition(s)

Name:
Intellectual disability
Synonyms:
Intellectual functioning disability; intellectual disabilities; Intellectual developmental disorder
Identifiers:
MONDO: MONDO:0001071; MeSH: D008607; MedGen: C3714756; Human Phenotype Ontology: HP:0001249

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001434468Diagnostic Laboratory, Strasbourg University Hospital
criteria provided, single submitter

(ACMG Guidelines, 2015)		Likely pathogenic
(Apr 20, 2020) 		de novoclinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedde novoyes1not providednot provided1noclinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee.

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]
PMID:
25741868
PMCID:
PMC4544753

Details of each submission

From Génétique des Maladies du Développement, Hospices Civils de Lyon, SCV000890065.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1de novoyesnot providednot providednot providednot providednot providednot providednot provided

From Diagnostic Laboratory, Strasbourg University Hospital, SCV001434468.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednoclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1de novoyes1bloodnot provided1not providednot providednot provided

Flagged submissions

Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000890065Génétique des Maladies du Développement, Hospices Civils de Lyon
flagged submission
Reason: Older and outlier claim with insufficient supporting evidence
Notes: None

(ACMG Guidelines, 2015)		Uncertain significance
(Sep 8, 2017) 		de novoclinical testing

PubMed (1)
[See all records that cite this PMID]

Last Updated: Apr 13, 2025