NM_024596.5:c.278C>A

Variant names:

• chr8-6431543-C-A
• rs587783741
• NM_024596.5:c.278C>A

Variant summary

Our verdict is Likely pathogenic. The variant received 7 ACMG points: 7P and 0B. PM1 PM2 PP3 PP5_Moderate

The NM_024596.5(MCPH1):​c.278C>A​(p.Ala93Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A93T) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 33)
• Consequence: MCPH1 NM_024596.5 missense
• Clinical Significance: Likely pathogenic criteria provided, single submitter P:1
• Conservation: PhyloP100: 3.53
• Publications: 0 publications found

Genes affected

MCPH1 (HGNC:6954): (microcephalin 1) This gene encodes a DNA damage response protein. The encoded protein may play a role in G2/M checkpoint arrest via maintenance of inhibitory phosphorylation of cyclin-dependent kinase 1. Mutations in this gene have been associated with primary autosomal recessive microcephaly 1 and premature chromosome condensation syndrome. Alternatively spliced transcript variants have been described. [provided by RefSeq, Feb 2010]

MCPH1 Gene-Disease associations (from GenCC):

• microcephaly 1, primary, autosomal recessive

  Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: G2P, Labcorp Genetics (formerly Invitae)
• microcephaly with intellectual disability

  Inheritance: AR Classification: DEFINITIVE Submitted by: ClinGen
• autosomal recessive primary microcephaly

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
• hereditary breast carcinoma

  Inheritance: AD Classification: LIMITED Submitted by: ClinGen
• familial ovarian cancer

  Inheritance: AD Classification: NO_KNOWN Submitted by: ClinGen

ACMG classification

Our verdict: Likely_pathogenic. The variant received 7 ACMG points.

• PM1: In a domain BRCT 1 (size 92) in uniprot entity MCPH1_HUMAN there are 9 pathogenic changes around while only 1 benign (90%) in NM_024596.5
• PM2: Very rare variant in population databases, with high coverage
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.773
• PP5: Variant 8-6431543-C-A is Pathogenic according to our data. Variant chr8-6431543-C-A is described in CliVar as Likely_pathogenic. Clinvar id is 158867.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr8-6431543-C-A is described in CliVar as Likely_pathogenic. Clinvar id is 158867.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr8-6431543-C-A is described in CliVar as Likely_pathogenic. Clinvar id is 158867.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr8-6431543-C-A is described in CliVar as Likely_pathogenic. Clinvar id is 158867.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr8-6431543-C-A is described in CliVar as Likely_pathogenic. Clinvar id is 158867.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr8-6431543-C-A is described in CliVar as Likely_pathogenic. Clinvar id is 158867.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr8-6431543-C-A is described in CliVar as Likely_pathogenic. Clinvar id is 158867.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr8-6431543-C-A is described in CliVar as Likely_pathogenic. Clinvar id is 158867.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr8-6431543-C-A is described in CliVar as Likely_pathogenic. Clinvar id is 158867.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr8-6431543-C-A is described in CliVar as Likely_pathogenic. Clinvar id is 158867.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr8-6431543-C-A is described in CliVar as Likely_pathogenic. Clinvar id is 158867.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr8-6431543-C-A is described in CliVar as Likely_pathogenic. Clinvar id is 158867.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr8-6431543-C-A is described in CliVar as Likely_pathogenic. Clinvar id is 158867.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr8-6431543-C-A is described in CliVar as Likely_pathogenic. Clinvar id is 158867.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr8-6431543-C-A is described in CliVar as Likely_pathogenic. Clinvar id is 158867.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr8-6431543-C-A is described in CliVar as Likely_pathogenic. Clinvar id is 158867.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr8-6431543-C-A is described in CliVar as Likely_pathogenic. Clinvar id is 158867.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr8-6431543-C-A is described in CliVar as Likely_pathogenic. Clinvar id is 158867.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr8-6431543-C-A is described in CliVar as Likely_pathogenic. Clinvar id is 158867.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr8-6431543-C-A is described in CliVar as Likely_pathogenic. Clinvar id is 158867.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr8-6431543-C-A is described in CliVar as Likely_pathogenic. Clinvar id is 158867.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr8-6431543-C-A is described in CliVar as Likely_pathogenic. Clinvar id is 158867.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr8-6431543-C-A is described in CliVar as Likely_pathogenic. Clinvar id is 158867.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr8-6431543-C-A is described in CliVar as Likely_pathogenic. Clinvar id is 158867.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr8-6431543-C-A is described in CliVar as Likely_pathogenic. Clinvar id is 158867.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MCPH1	NM_024596.5	c.278C>A	p.Ala93Glu	missense_variant	Exon 4 of 14	ENST00000344683.10	NP_078872.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MCPH1	ENST00000344683.10	c.278C>A	p.Ala93Glu	missense_variant	Exon 4 of 14	1	NM_024596.5	ENSP00000342924.5

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 29

GnomAD4 genome Cov.: 33

Alfa AF: 0.00000497 Hom.: 0

ClinVar

Significance: Likely pathogenic

Submissions summary: Pathogenic:1

Revision: criteria provided, single submitter

Submissions by phenotype

Microcephaly 1, primary, autosomal recessive Pathogenic:1

Feb 08, 2013

Genetic Services Laboratory, University of Chicago

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.84
BayesDel_addAF	Pathogenic	0.17	D
BayesDel_noAF	Uncertain	0.010
CADD	Uncertain	25
DANN	Uncertain	0.99
DEOGEN2	Uncertain	0.61	D;.;.
Eigen	Uncertain	0.61
Eigen_PC	Uncertain	0.54
FATHMM_MKL	Uncertain	0.96	D
M_CAP	Benign	0.043	D
MetaRNN	Pathogenic	0.77	D;D;D
MetaSVM	Benign	-0.39	T
MutationAssessor	Uncertain	2.7	M;M;M
PhyloP100		3.5
PrimateAI	Benign	0.48	T
PROVEAN	Uncertain	-3.2	D;D;D
REVEL	Uncertain	0.29
Sift	Uncertain	0.0010	D;D;D
Sift4G	Uncertain	0.0090	D;D;D
Polyphen		1.0	D;.;.
Vest4		0.67
MutPred		0.47		Gain of solvent accessibility (P = 9e-04);Gain of solvent accessibility (P = 9e-04);Gain of solvent accessibility (P = 9e-04);
MVP		0.76
ClinPred		0.99	D
GERP RS		5.3
Varity_R		0.90
gMVP		0.62
Mutation Taster		=30/70	disease causing (ClinVar)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs587783741; hg19: chr8-6289064;