4-110621210-C-T

Variant names:

• chr4-110621210-C-T
• rs104893861
• NM_000325.6:c.365G>A

Variant summary

Our verdict is Pathogenic. Variant got 10 ACMG points: 10P and 0B. PM1 PM2 PP3_Strong PP5_Moderate

The NM_000325.6(PITX2):​c.365G>A​(p.Arg122His) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. 13/21 in silico tools predict a damaging outcome for this variant. Variant has been reported in ClinVar as Pathogenic (★).

• Frequency: Genomes: not found (cov: 33)
• Consequence: PITX2 NM_000325.6 missense
• Clinical Significance: Pathogenic criteria provided, single submitter P:2
• Conservation: PhyloP100: 7.83

Genes affected

PITX2 (HGNC:9005): (paired like homeodomain 2) This gene encodes a member of the RIEG/PITX homeobox family, which is in the bicoid class of homeodomain proteins. The encoded protein acts as a transcription factor and regulates procollagen lysyl hydroxylase gene expression. This protein plays a role in the terminal differentiation of somatotroph and lactotroph cell phenotypes, is involved in the development of the eye, tooth and abdominal organs, and acts as a transcriptional regulator involved in basal and hormone-regulated activity of prolactin. Mutations in this gene are associated with Axenfeld-Rieger syndrome, iridogoniodysgenesis syndrome, and sporadic cases of Peters anomaly. A similar protein in other vertebrates is involved in the determination of left-right asymmetry during development. Alternatively spliced transcript variants encoding distinct isoforms have been described. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Pathogenic. Variant got 10 ACMG points.

• PM1: In a DNA_binding_region Homeobox (size 59) in uniprot entity PITX2_HUMAN there are 15 pathogenic changes around while only 0 benign (100%) in NM_000325.6
• PM2: Very rare variant in population databases, with high coverage
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.986
• PP5: Variant 4-110621210-C-T is Pathogenic according to our data. Variant chr4-110621210-C-T is described in ClinVar as [Pathogenic]. Clinvar id is 8090.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PITX2	NM_000325.6	c.365G>A	p.Arg122His	missense_variant	Exon 2 of 3	ENST00000644743.1	NP_000316.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PITX2	ENST00000644743.1	c.365G>A	p.Arg122His	missense_variant	Exon 2 of 3		NM_000325.6	ENSP00000495061.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 33

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:2

Revision: criteria provided, single submitter

Submissions by phenotype

Anterior segment dysgenesis 4 Pathogenic:1

Jul 01, 1998

OMIM

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: literature only

- -

not provided Pathogenic:1

Jan 28, 2016

GeneDx

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The R115H missense variant in the PITX2 gene has been reported previously in association with iridogoniodysgenesis syndrome (Kulak et al., 1998). The variant was not observed in approximately 6,500 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, indicating it is not a common benign variant in these populations. This substitution occurs at a position in the second helix of the homeobox domain that is conserved across species, and functional studies have shown R115H has a significant detrimental effect on the activity of the PITX2 protein (Quentien et al., 2002). Quentien et al. hypothesized that R115 is the only residue within the second helix that provides a DNA contact and therefore might be critical in the stabilization of the folded protein-DNA complex. Missense variants in the same codon (R115C) and in nearby residues (P110R/L, T114P) have been reported in the Human Gene Mutation Database in association with PITX2-related disorders (Stenson et al., 2014), supporting the functional importance of this region of the protein. We interpret this variant to be pathogenic. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	1.0
BayesDel_addAF	Pathogenic	0.57	D
BayesDel_noAF	Pathogenic	0.58
CADD	Pathogenic	34
DANN	Pathogenic	1.0
DEOGEN2	Pathogenic	0.99	.;.;D;D;.;D;D;D;.;D;.;.
Eigen	Pathogenic	0.90
Eigen_PC	Pathogenic	0.79
FATHMM_MKL	Pathogenic	0.97	D
LIST_S2	Uncertain	0.96	.;D;.;.;.;.;.;D;D;D;D;D
M_CAP	Pathogenic	0.72	D
MetaRNN	Pathogenic	0.99	D;D;D;D;D;D;D;D;D;D;D;D
MetaSVM	Pathogenic	1.0	D
MutationAssessor	Pathogenic	3.9	.;.;H;H;.;H;H;H;.;.;.;.
PrimateAI	Pathogenic	0.93	D
PROVEAN	Pathogenic	-4.7	.;D;.;D;D;D;.;.;.;D;D;.
REVEL	Pathogenic	0.95
Sift	Pathogenic	0.0	.;D;.;D;D;D;.;.;.;D;D;.
Sift4G	Pathogenic	0.0010	.;D;.;D;D;D;D;D;D;D;.;D
Polyphen		1.0	D;D;D;D;B;D;D;D;B;D;.;.
Vest4		0.94, 0.94, 0.91, 0.94, 0.91, 0.74
MutPred		0.95		.;.;Loss of MoRF binding (P = 0.0246);Loss of MoRF binding (P = 0.0246);.;Loss of MoRF binding (P = 0.0246);Loss of MoRF binding (P = 0.0246);Loss of MoRF binding (P = 0.0246);.;Loss of MoRF binding (P = 0.0246);.;.;
MVP		0.98
MPC		2.2
ClinPred		1.0	D
GERP RS		4.5
Varity_R		0.94
gMVP		0.98

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

Publications

LitVar

Other links and lift over

dbSNP: rs104893861; hg19: chr4-111542366;