9-124014022-CGGACC-ACCT

Position:

• chr9-124014022-CGGACC-ACCT

Variant summary

Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2 PP5_Moderate

The NM_004789.4(LHX2):​c.182_187delCGGACCinsACCT​(p.Ser61fs) variant causes a frameshift, missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Likely pathogenic (★). Variant results in nonsense mediated mRNA decay.

• Frequency: Genomes: not found (cov: 33)
• Consequence: LHX2 NM_004789.4 frameshift, missense
• Clinical Significance: Likely pathogenic criteria provided, single submitter P:1
• Conservation: PhyloP100: 10.0

Genes affected

LHX2 (HGNC:6594): (LIM homeobox 2) This gene encodes a protein belonging to a large protein family, members of which carry the LIM domain, a unique cysteine-rich zinc-binding domain. The encoded protein may function as a transcriptional regulator. The protein can recapitulate or rescue phenotypes in Drosophila caused by a related protein, suggesting conservation of function during evolution. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Uncertain_significance. Variant got 4 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PP5: Variant 9-124014022-CGGACC-ACCT is Pathogenic according to our data. Variant chr9-124014022-CGGACC-ACCT is described in ClinVar as [Likely_pathogenic]. Clinvar id is 2572331.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LHX2	NM_004789.4	c.182_187delCGGACCinsACCT	p.Ser61fs	frameshift_variant, missense_variant	2/5	ENST00000373615.9	NP_004780.3
LHX2	XM_006717323.4	c.182_187delCGGACCinsACCT	p.Ser61fs	frameshift_variant, missense_variant	2/6		XP_006717386.1
LHX2	XM_047424082.1	c.182_187delCGGACCinsACCT	p.Ser61fs	frameshift_variant, missense_variant	2/6		XP_047280038.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LHX2	ENST00000373615.9	c.182_187delCGGACCinsACCT	p.Ser61fs	frameshift_variant, missense_variant	2/5	1	NM_004789.4	ENSP00000362717.4
LHX2	ENST00000446480.5	c.173_178delCGGACCinsACCT	p.Ser58fs	frameshift_variant, missense_variant	2/5	2		ENSP00000394978.1
LHX2	ENST00000560961.2	c.59_64delCGGACCinsACCT	p.Ser20fs	frameshift_variant, missense_variant	2/3	3		ENSP00000453448.3

Frequencies

GnomAD3 genomes Cov.: 33

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Cov.: 33

ClinVar

Significance: Likely pathogenic

Submissions summary: Pathogenic:1

Revision: criteria provided, single submitter

Submissions by phenotype

Variable neurodevelopmental disorder Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

Greenwood Genetic Center Diagnostic Laboratories, Greenwood Genetic Center

Apr 14, 2023

PVS1, PM2 -

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: chr9-126776301;