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NM_024596.5(MCPH1):c.1349A>C (p.Lys450Thr) AND not provided

Germline classification:
Conflicting interpretations of pathogenicity (3 submissions)
Last evaluated:
Jan 24, 2024
Review status:
criteria provided, conflicting classifications
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:
RCV000594510.23

Allele description [Variation Report for NM_024596.5(MCPH1):c.1349A>C (p.Lys450Thr)]

NM_024596.5(MCPH1):c.1349A>C (p.Lys450Thr)

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.1349A>C (p.Lys450Thr)
HGVS:
  • NC_000008.11:g.6445071A>C
  • NG_016619.2:g.43480A>C
  • NM_001172574.2:c.1349A>C
  • NM_001172575.2:c.1205A>C
  • NM_001322042.1:c.1349A>C
  • NM_001322042.2:c.1349A>C
  • NM_001322043.2:c.1343A>C
  • NM_001322045.2:c.1247A>C
  • NM_001363979.1:c.1349A>C
  • NM_001363980.2:c.1349A>C
  • NM_024596.5:c.1349A>CMANE SELECT
  • NP_001166045.2:p.Lys450Thr
  • NP_001166046.1:p.Lys402Thr
  • NP_001308971.2:p.Lys450Thr
  • NP_001308972.2:p.Lys448Thr
  • NP_001308974.2:p.Lys416Thr
  • NP_001350908.1:p.Lys450Thr
  • NP_001350909.1:p.Lys450Thr
  • NP_078872.3:p.Lys450Thr
  • NC_000008.10:g.6302592A>C
  • NM_024596.3:c.1349A>C
  • NM_024596.4:c.1349A>C
  • NR_136159.2:n.1275A>C
Protein change:
K402T
Links:
dbSNP: rs77959215
NCBI 1000 Genomes Browser:
rs77959215
Molecular consequence:
  • NM_001172574.2:c.1349A>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001172575.2:c.1205A>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001322042.2:c.1349A>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001322043.2:c.1343A>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001322045.2:c.1247A>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001363979.1:c.1349A>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001363980.2:c.1349A>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_024596.5:c.1349A>C - missense variant - [Sequence Ontology: SO:0001583]
  • NR_136159.2:n.1275A>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
Observations:
4

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000705396Eurofins Ntd Llc (ga)
criteria provided, single submitter

(EGL Classification Definitions 2015)
Uncertain significance
(Jan 26, 2017)
germlineclinical testing

Citation Link,

SCV001043968Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))
Benign
(Jan 24, 2024)
germlineclinical testing

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

SCV004159479CeGaT Center for Human Genetics Tuebingen
criteria provided, single submitter

(CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)
Likely benign
(May 1, 2023)
germlineclinical testing

Citation Link

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyes1not providednot providednot providednot providedclinical testing
not providedgermlineunknown3not 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. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Eurofins Ntd Llc (ga), SCV000705396.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided3not providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot provided3not providednot providednot provided

From Labcorp Genetics (formerly Invitae), Labcorp, SCV001043968.4

#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 CeGaT Center for Human Genetics Tuebingen, SCV004159479.10

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testingnot provided

Description

MCPH1: BP4

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

Last Updated: Oct 20, 2024