7-157005528-G-GCGCGGGCTGGTGGCTGGGC

Variant summary

Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2 PM4 PP5_Moderate

The NM_005515.4(MNX1):c.1197_1198insGCCCAGCCACCAGCCCGCG(p.Pro400AlafsTer73) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Likely pathogenic (★).

• Frequency: Genomes: not found (cov: 33)
• Consequence: MNX1 NM_005515.4 frameshift
• Clinical Significance: Likely pathogenic criteria provided, single submitter P:1
• Conservation: PhyloP100: -0.100

Genes affected

MNX1 (HGNC:4979): (motor neuron and pancreas homeobox 1) This gene encodes a nuclear protein, which contains a homeobox domain and is a transcription factor. Mutations in this gene result in Currarino syndrome, an autosomic dominant congenital malformation. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2009]

ACMG classification

Verdict is Likely_pathogenic. Variant got 6 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PM4: Frameshift in the end of transcript resulting in stoplost. Downstream stopcodon found after 459 codons.
• PP5: Variant 7-157005528-G-GCGCGGGCTGGTGGCTGGGC is Pathogenic according to our data. Variant chr7-157005528-G-GCGCGGGCTGGTGGCTGGGC is described in ClinVar as [Likely_pathogenic]. Clinvar id is 2636432.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MNX1	NM_005515.4	c.1197_1198insGCCCAGCCACCAGCCCGCG	p.Pro400AlafsTer73	frameshift_variant	3/3	ENST00000252971.11
MNX1	NM_001165255.2	c.561_562insGCCCAGCCACCAGCCCGCG	p.Pro188AlafsTer73	frameshift_variant	3/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MNX1	ENST00000252971.11	c.1197_1198insGCCCAGCCACCAGCCCGCG	p.Pro400AlafsTer73	frameshift_variant	3/3	1	NM_005515.4	P2
MNX1	ENST00000543409.5	c.561_562insGCCCAGCCACCAGCCCGCG	p.Pro188AlafsTer73	frameshift_variant	3/3	1		A2
MNX1	ENST00000469500.5	c.55+3469_55+3470insGCCCAGCCACCAGCCCGCG		intron_variant		1
MNX1	ENST00000479817.1	c.38+4131_38+4132insGCCCAGCCACCAGCCCGCG		intron_variant		1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 33

ClinVar

Significance: Likely pathogenic

Submissions summary: Pathogenic:1

Revision: criteria provided, single submitter

Submissions by phenotype

MNX1-related disorder Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

Sep 06, 2022

The MNX1 c.1179_1197dup19 variant is predicted to result in a frameshift and premature protein termination (p.Pro400Alafs*73). This variant occurs in the last exon of MNX1, near the native stop codon and is predicted to result in a frameshift and protein extension. To our knowledge, this variant has not been reported in the literature or in a large population database (http://gnomad.broadinstitute.org), indicating this variant is rare. Downstream, a similar MNX1 insertion affecting the translation termination codon was reported in a family with Currarino syndrome (c.1205insCACCAGCCCGCGCCCCAGT p.X402Serfs70, Han et al. 2020. PubMed ID: 32571425). Both the previously-reported stop-loss variant and the duplication variant reported here, are predicted to result in an insertion and 1-basepair shift in the reading-frame resulting in a nearly identical protein extension. Taken together, the c.1179_1197dup19 (p.Pro400Alafs*73) variant is interpreted as likely pathogenic. -

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr7-156798222;