NM_005029.4:c.738_740delCGC

Variant summary

Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP3BS2

The NM_005029.4(PITX3):​c.738_740delCGC​(p.Ala247del) variant causes a disruptive inframe deletion change. The variant allele was found at a frequency of 0.0000806 in 1,575,464 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: 𝑓 0.000020 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000087 ( 0 hom. )

Consequence

PITX3
NM_005029.4 disruptive_inframe_deletion

Scores

Not classified

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 4.42
Variant links:
Genes affected
PITX3 (HGNC:9006): (paired like homeodomain 3) This gene encodes a member of the RIEG/PITX homeobox family, which is in the bicoid class of homeodomain proteins. Members of this family act as transcription factors. This protein is involved in lens formation during eye development. Mutations of this gene have been associated with anterior segment mesenchymal dysgenesis and congenital cataracts. [provided by RefSeq, Jul 2008]
GBF1 (HGNC:4181): (golgi brefeldin A resistant guanine nucleotide exchange factor 1) This gene encodes a member of the Sec7 domain family. The encoded protein is a guanine nucleotide exchange factor that regulates the recruitment of proteins to membranes by mediating GDP to GTP exchange. The encoded protein is localized to the Golgi apparatus and plays a role in vesicular trafficking by activating ADP ribosylation factor 1. The encoded protein has also been identified as an important host factor for viral replication. Multiple transcript variants have been observed for this gene. [provided by RefSeq, Dec 2010]

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -5 ACMG points.

BP3
Nonframeshift variant in repetitive region in NM_005029.4
BS2
High AC in GnomAdExome4 at 124 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
PITX3NM_005029.4 linkc.738_740delCGC p.Ala247del disruptive_inframe_deletion Exon 4 of 4 ENST00000370002.8 NP_005020.1
PITX3XM_047425352.1 linkc.738_740delCGC p.Ala247del disruptive_inframe_deletion Exon 3 of 3 XP_047281308.1
GBF1NM_001391923.1 linkc.-230_-228delGGC 5_prime_UTR_variant Exon 1 of 40 NP_001378852.1
GBF1NM_001391924.1 linkc.-368_-366delGGC 5_prime_UTR_variant Exon 1 of 41 NP_001378853.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
PITX3ENST00000370002.8 linkc.738_740delCGC p.Ala247del disruptive_inframe_deletion Exon 4 of 4 1 NM_005029.4 ENSP00000359019.3 O75364

Frequencies

GnomAD3 genomes
AF:
0.0000197
AC:
3
AN:
152096
Hom.:
0
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000441
Gnomad OTH
AF:
0.00
GnomAD4 exome
AF:
0.0000871
AC:
124
AN:
1423368
Hom.:
0
AF XY:
0.0000922
AC XY:
65
AN XY:
705066
show subpopulations
Gnomad4 AFR exome
AF:
0.000246
Gnomad4 AMR exome
AF:
0.0000523
Gnomad4 ASJ exome
AF:
0.0000394
Gnomad4 EAS exome
AF:
0.000213
Gnomad4 SAS exome
AF:
0.0000489
Gnomad4 FIN exome
AF:
0.0000601
Gnomad4 NFE exome
AF:
0.0000860
Gnomad4 OTH exome
AF:
0.0000678
GnomAD4 genome
AF:
0.0000197
AC:
3
AN:
152096
Hom.:
0
Cov.:
33
AF XY:
0.0000135
AC XY:
1
AN XY:
74302
show subpopulations
Gnomad4 AFR
AF:
0.00
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000441
Gnomad4 OTH
AF:
0.00

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Uncertain:1
Oct 31, 2024
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing

This variant, c.738_740del, results in the deletion of 1 amino acid(s) of the PITX3 protein (p.Ala250del), but otherwise preserves the integrity of the reading frame. The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This variant has not been reported in the literature in individuals affected with PITX3-related conditions. Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs749538425; hg19: chr10-103990439; API