Variant chr5-135033815-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2

The NM_002653.5(PITX1):c.67C>T(p.Pro23Ser) variant causes a missense change. The variant allele was found at a frequency of 0.00000434 in 1,383,888 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 31)

Exomes 𝑓: 0.0000043 ( 0 hom. )

Consequence

PITX1
NM_002653.5 missense

Scores

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 4.55

Variant links:

Genes affected

PITX1 (HGNC:9004): (paired like homeodomain 1) This gene encodes a member of the RIEG/PITX homeobox family, which is in the bicoid class of homeodomain proteins. Members of this family are involved in organ development and left-right asymmetry. This protein acts as a transcriptional regulator involved in basal and hormone-regulated activity of prolactin. [provided by RefSeq, Jul 2008]

PITX1 links:

PITX1-AS1 (HGNC:48332): (PITX1 antisense RNA 1)

PITX1-AS1 links:

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -6 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.1915327).

BS2

High AC in GnomAdExome4 at 6 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE
PITX1	NM_002653.5 linkuse as main transcript	c.67C>T	p.Pro23Ser	missense_variant	1/3	ENST00000265340.12
PITX1-AS1	NR_161235.1 linkuse as main transcript	n.267+275G>A		intron_variant, non_coding_transcript_variant
PITX1	XM_047417318.1 linkuse as main transcript	c.169C>T	p.Pro57Ser	missense_variant	2/4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PITX1	ENST00000265340.12 linkuse as main transcript	c.67C>T	p.Pro23Ser	missense_variant	1/3	1	NM_002653.5	P1
PITX1-AS1	ENST00000624272.3 linkuse as main transcript	n.261+275G>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

AF:

0.00000434

AC:

AN:

1383888

Hom.:

Cov.:

AF XY:

0.00000729

AC XY:

AN XY:

685982

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.00000185

Gnomad4 OTH exome

AF:

0.0000696

GnomAD4 genome

Cov.:

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Ambry Genetics

Jun 02, 2023

The c.67C>T (p.P23S) alteration is located in exon 1 (coding exon 1) of the PITX1 gene. This alteration results from a C to T substitution at nucleotide position 67, causing the proline (P) at amino acid position 23 to be replaced by a serine (S). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.072

BayesDel_addAF

Uncertain

0.043

BayesDel_noAF

Benign

-0.18

CADD

Benign

DANN

Uncertain

0.98

DEOGEN2

Benign

0.18

T;T;.;T

Eigen

Benign

-0.69

Eigen_PC

Benign

-0.64

FATHMM_MKL

Uncertain

0.91

LIST_S2

Benign

0.50

.;T;T;T

M_CAP

Pathogenic

0.90

MetaRNN

Benign

0.19

T;T;T;T

MetaSVM

Benign

-0.46

MutationAssessor

Benign

0.76

N;N;.;.

MutationTaster

Benign

0.99

N;N

PrimateAI

Pathogenic

0.89

PROVEAN

Benign

-0.17

N;N;N;N

REVEL

Benign

0.17

Sift

Benign

0.47

T;T;T;T

Sift4G

Benign

0.95

T;T;.;T

Polyphen

0.0060

B;B;.;.

Vest4

0.20

MutPred

0.28

Gain of phosphorylation at P23 (P = 0.006);Gain of phosphorylation at P23 (P = 0.006);Gain of phosphorylation at P23 (P = 0.006);Gain of phosphorylation at P23 (P = 0.006);

MVP

0.93

MPC

1.0

ClinPred

0.19

GERP RS

1.3

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

2.4

Varity_R

0.055

gMVP

0.37

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

No publications associated with this variant yet.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over