NM_024596.5(MCPH1):c.1403C>A (p.Thr468Asn) AND not provided

Clinical significance:Conflicting interpretations of pathogenicity, Likely benign(1);Uncertain significance(1) (Last evaluated: Sep 18, 2018)

Review status:1 star out of maximum of 4 stars

criteria provided, conflicting interpretations

Based on:
2 submissions [Details]
Record status:
current
Accession:
RCV000930721.2

Allele description [Variation Report for NM_024596.5(MCPH1):c.1403C>A (p.Thr468Asn)]

NM_024596.5(MCPH1):c.1403C>A (p.Thr468Asn)

Gene:
MCPH1:microcephalin 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
8p23.1
Genomic location:
Preferred name:
NM_024596.5(MCPH1):c.1403C>A (p.Thr468Asn)
HGVS:
  • NC_000008.11:g.6445125C>A
  • NG_016619.2:g.43534C>A
  • NM_001172574.1:c.1403C>A
  • NM_001172575.1:c.1259C>A
  • NM_001322042.2:c.1403C>A
  • NM_001322043.1:c.1397C>A
  • NM_001322045.1:c.1301C>A
  • NM_001363979.1:c.1403C>A
  • NM_001363980.2:c.1403C>A
  • NM_024596.5:c.1403C>AMANE SELECT
  • NP_001166045.1:p.Thr468Asn
  • NP_001166046.1:p.Thr420Asn
  • NP_001308971.2:p.Thr468Asn
  • NP_001308972.1:p.Thr466Asn
  • NP_001308974.1:p.Thr434Asn
  • NP_001350908.1:p.Thr468Asn
  • NP_001350909.1:p.Thr468Asn
  • NP_078872.3:p.Thr468Asn
  • NC_000008.10:g.6302646C>A
  • NM_024596.3:c.1403C>A
  • NM_024596.4:c.1403C>A
  • NR_136159.1:n.1364C>A
Protein change:
T420N
Links:
dbSNP: rs548329168
NCBI 1000 Genomes Browser:
rs548329168
Molecular consequence:
  • NM_001172574.1:c.1403C>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001172575.1:c.1259C>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001322042.2:c.1403C>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001322043.1:c.1397C>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001322045.1:c.1301C>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001363979.1:c.1403C>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001363980.2:c.1403C>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_024596.5:c.1403C>A - missense variant - [Sequence Ontology: SO:0001583]
  • NR_136159.1:n.1364C>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Identifiers:
MedGen: CN517202

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV001076377Invitaecriteria provided, single submitter
Likely benign
(Jun 15, 2018)
germlineclinical testing

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

SCV001144486Athena Diagnostics Inccriteria provided, single submitter
Uncertain significance
(Sep 18, 2018)
germlineclinical testing

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

Summary from all submissions

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

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240-242.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

A Standardized DNA Variant Scoring System for Pathogenicity Assessments in Mendelian Disorders.

Karbassi I, Maston GA, Love A, DiVincenzo C, Braastad CD, Elzinga CD, Bright AR, Previte D, Zhang K, Rowland CM, McCarthy M, Lapierre JL, Dubois F, Medeiros KA, Batish SD, Jones J, Liaquat K, Hoffman CA, Jaremko M, Wang Z, Sun W, Buller-Burckle A, et al.

Hum Mutat. 2016 Jan;37(1):127-34. doi: 10.1002/humu.22918. Epub 2015 Oct 29.

PubMed [citation]
PMID:
26467025
PMCID:
PMC4737317

Details of each submission

From Invitae, SCV001076377.1

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

From Athena Diagnostics Inc, SCV001144486.1

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

Last Updated: May 27, 2021

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