Variant 1-213996953-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2

The NM_001270616.2(PROX1):c.418T>C(p.Cys140Arg) variant causes a missense change. The variant allele was found at a frequency of 0.00000684 in 1,461,892 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 32)

Exomes 𝑓: 0.0000068 ( 0 hom. )

Consequence

PROX1
NM_001270616.2 missense

Scores

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 5.82

Variant links:

Genes affected

PROX1 (HGNC:9459): (prospero homeobox 1) The protein encoded by this gene is a member of the homeobox transcription factor family. Members of this family contain a homeobox domain that consists of a 60-amino acid helix-turn-helix structure that binds DNA and RNA. The protein encoded by this gene is conserved across vertebrates and may play an essential role during development. Altered levels of this protein have been reported in cancers of different organs, such as colon, brain, blood, breast, pancreas, liver and esophagus. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2012]

PROX1 links:

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -4 ACMG points.

BS2

High AC in GnomAdExome4 at 10 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PROX1	NM_001270616.2 linkuse as main transcript	c.418T>C	p.Cys140Arg	missense_variant	2/5	ENST00000366958.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris
PROX1	ENST00000366958.9 linkuse as main transcript	c.418T>C	p.Cys140Arg	missense_variant	2/5	1	NM_001270616.2	P1
PROX1	ENST00000435016.2 linkuse as main transcript	c.418T>C	p.Cys140Arg	missense_variant	2/5	1		P1
PROX1	ENST00000471129.1 linkuse as main transcript	c.418T>C	p.Cys140Arg	missense_variant	2/2	3
PROX1	ENST00000607425.1 linkuse as main transcript	c.418T>C	p.Cys140Arg	missense_variant	2/2	3

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

AF:

0.00000684

AC:

AN:

1461892

Hom.:

Cov.:

AF XY:

0.00000688

AC XY:

AN XY:

727246

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:

0.00000809

Gnomad4 OTH exome

AF:

0.0000166

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

Jan 18, 2023

The c.418T>C (p.C140R) alteration is located in exon 2 (coding exon 1) of the PROX1 gene. This alteration results from a T to C substitution at nucleotide position 418, causing the cysteine (C) at amino acid position 140 to be replaced by an arginine (R). 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

0.24

BayesDel_addAF

Uncertain

0.073

BayesDel_noAF

Benign

-0.13

CADD

Uncertain

DANN

Uncertain

0.99

DEOGEN2

Benign

0.20

.;T;T;T;T;.

Eigen

Uncertain

0.66

Eigen_PC

Pathogenic

0.67

FATHMM_MKL

Uncertain

0.97

LIST_S2

Uncertain

0.90

D;.;.;D;.;T

M_CAP

Benign

0.032

MetaRNN

Uncertain

0.56

D;D;D;D;D;D

MetaSVM

Benign

-1.1

MutationAssessor

Benign

1.1

.;L;L;L;L;.

MutationTaster

Benign

1.0

D;D;D

PrimateAI

Pathogenic

0.85

PROVEAN

Benign

-2.2

N;N;N;N;N;.

REVEL

Benign

0.28

Sift

Benign

0.14

T;T;D;T;T;.

Sift4G

Pathogenic

0.0

D;T;T;T;T;D

Polyphen

1.0

.;D;D;D;D;.

Vest4

0.82, 0.82, 0.82, 0.82

MutPred

0.48

Loss of catalytic residue at L141 (P = 0.0334);Loss of catalytic residue at L141 (P = 0.0334);Loss of catalytic residue at L141 (P = 0.0334);Loss of catalytic residue at L141 (P = 0.0334);Loss of catalytic residue at L141 (P = 0.0334);Loss of catalytic residue at L141 (P = 0.0334);

MVP

0.55

MPC

2.2

ClinPred

0.92

GERP RS

5.6

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Varity_R

0.64

gMVP

0.53

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