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NM_024596.5(MCPH1):c.1236T>C (p.Tyr412=)

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Interpretation:
Benign/Likely benign​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
4 (Most recent: Jan 29, 2020)
Last evaluated:
Dec 31, 2019
Accession:
VCV000096127.3
Variation ID:
96127
Description:
single nucleotide variant
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NM_024596.5(MCPH1):c.1236T>C (p.Tyr412=)

Allele ID
102021
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
8p23.1
Genomic location
8: 6444958 (GRCh38) GRCh38 UCSC
8: 6302479 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000008.10:g.6302479T>C
NC_000008.11:g.6444958T>C
NM_024596.5:c.1236T>C MANE Select NP_078872.3:p.Tyr412= synonymous
... more HGVS
Protein change
-
Other names
-
Canonical SPDI
NC_000008.11:6444957:T:C
Functional consequence
-
Global minor allele frequency (GMAF)
0.00200 (C)

Allele frequency
Exome Aggregation Consortium (ExAC) 0.00036
The Genome Aggregation Database (gnomAD) 0.00099
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00097
The Genome Aggregation Database (gnomAD), exomes 0.00029
1000 Genomes Project 0.00200
Trans-Omics for Precision Medicine (TOPMed) 0.00124
Links
ClinGen: CA149262
dbSNP: rs142858644
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Benign/Likely benign 3 criteria provided, multiple submitters, no conflicts Feb 12, 2016 RCV000082199.8
Benign 1 criteria provided, single submitter Dec 31, 2019 RCV000899683.2
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
MCPH1 - - GRCh38
GRCh38
GRCh37
239 477

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely benign
(Dec 03, 2013)
criteria provided, single submitter
Method: clinical testing
not specified
(Autosomal recessive inheritance)
Allele origin: germline
Genetic Services Laboratory, University of Chicago
Accession: SCV000193535.1
Submitted: (Sep 11, 2014)
Comment:
Likely benign based on allele frequency in 1000 Genomes Project or ESP global frequency and its presence in a patient with a rare or unrelated … (more)
Evidence details
Likely benign
(Feb 12, 2016)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
GeneDx
Accession: SCV000524107.4
Submitted: (Mar 26, 2018)
Evidence details
Comment:
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at … (more)
Benign
(Aug 09, 2013)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000114148.8
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
http://www.ncbi.nlm.nih.gov/vari…
Benign
(Dec 31, 2019)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Invitae
Accession: SCV001043967.2
Submitted: (Jan 29, 2020)
Evidence details

Functional evidence

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There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Text-mined citations for rs142858644...

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These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated May 27, 2021