chr3-189866712-G-A

Variant names:

Variant summary

Our verdict is Pathogenic. The variant received 19 ACMG points: 19P and 0B. PM1PM2PM5PP2PP3_StrongPP5_Very_Strong

The NM_003722.5(TP63):c.797G>A(p.Arg266Gln) 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. Variant has been reported in ClinVar as Likely pathogenic (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R266G) has been classified as Likely pathogenic.

Frequency

Genomes: not found (cov: 32)

Consequence

TP63
NM_003722.5 missense

Scores

Clinical Significance

Pathogenic/Likely pathogenic criteria provided, multiple submitters, no conflicts P:8

Conservation

PhyloP100: 9.90

Publications

14 publications found

Variant links:

Genes affected

TP63 (HGNC:15979): (tumor protein p63) This gene encodes a member of the p53 family of transcription factors. The functional domains of p53 family proteins include an N-terminal transactivation domain, a central DNA-binding domain and an oligomerization domain. Alternative splicing of this gene and the use of alternative promoters results in multiple transcript variants encoding different isoforms that vary in their functional properties. These isoforms function during skin development and maintenance, adult stem/progenitor cell regulation, heart development and premature aging. Some isoforms have been found to protect the germline by eliminating oocytes or testicular germ cells that have suffered DNA damage. Mutations in this gene are associated with ectodermal dysplasia, and cleft lip/palate syndrome 3 (EEC3); split-hand/foot malformation 4 (SHFM4); ankyloblepharon-ectodermal defects-cleft lip/palate; ADULT syndrome (acro-dermato-ungual-lacrimal-tooth); limb-mammary syndrome; Rap-Hodgkin syndrome (RHS); and orofacial cleft 8. [provided by RefSeq, Aug 2016]

TP63 Gene-Disease associations (from GenCC):

ADULT syndrome
Inheritance: AD Classification: DEFINITIVE, SUPPORTIVE Submitted by: G2P, Orphanet
ankyloblepharon-ectodermal defects-cleft lip/palate syndrome
Inheritance: AD Classification: DEFINITIVE, SUPPORTIVE Submitted by: G2P, Orphanet
ectrodactyly, ectodermal dysplasia, and cleft lip-palate syndrome 3
Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: Ambry Genetics, Labcorp Genetics (formerly Invitae)
limb-mammary syndrome
Inheritance: AD Classification: DEFINITIVE, SUPPORTIVE Submitted by: G2P, Orphanet
Rapp-Hodgkin syndrome
Inheritance: AD Classification: DEFINITIVE Submitted by: G2P
premature ovarian failure 21
Inheritance: AD Classification: STRONG, MODERATE Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics
split hand-foot malformation 4
Inheritance: AD Classification: MODERATE Submitted by: Illumina
EEC syndrome
Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
split hand-foot malformation
Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

TP63 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Pathogenic. The variant received 19 ACMG points.

PM1

In a strand (size 6) in uniprot entity P63_HUMAN there are 5 pathogenic changes around while only 0 benign (100%) in NM_003722.5

PM2

Very rare variant in population databases, with high coverage;

PM5

Other missense variant is known to change same aminoacid residue: Variant chr3-189866711-C-G is described in CliVar as Likely_pathogenic. Clinvar id is 3602938.Status of the report is criteria_provided_single_submitter, 1 stars.

PP2

Missense variant in the TP63 gene, where missense mutations are typically associated with disease (based on misZ statistic). The gene has 73 curated pathogenic missense variants (we use a threshold of 10). The gene has 15 curated benign missense variants. Gene score misZ: 2.2077 (below the threshold of 3.09). Trascript score misZ: 3.5096 (above the threshold of 3.09). GenCC associations: The gene is linked to Rapp-Hodgkin syndrome, ADULT syndrome, premature ovarian failure 21, limb-mammary syndrome, ectrodactyly, ectodermal dysplasia, and cleft lip-palate syndrome 3, ankyloblepharon-ectodermal defects-cleft lip/palate syndrome, EEC syndrome, split hand-foot malformation, split hand-foot malformation 4.

PP3

MetaRNN computational evidence supports a deleterious effect, 0.988

PP5

Variant 3-189866712-G-A is Pathogenic according to our data. Variant chr3-189866712-G-A is described in CliVar as Pathogenic/Likely_pathogenic. Clinvar id is 6550.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-189866712-G-A is described in CliVar as Pathogenic/Likely_pathogenic. Clinvar id is 6550.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-189866712-G-A is described in CliVar as Pathogenic/Likely_pathogenic. Clinvar id is 6550.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-189866712-G-A is described in CliVar as Pathogenic/Likely_pathogenic. Clinvar id is 6550.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-189866712-G-A is described in CliVar as Pathogenic/Likely_pathogenic. Clinvar id is 6550.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-189866712-G-A is described in CliVar as Pathogenic/Likely_pathogenic. Clinvar id is 6550.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-189866712-G-A is described in CliVar as Pathogenic/Likely_pathogenic. Clinvar id is 6550.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-189866712-G-A is described in CliVar as Pathogenic/Likely_pathogenic. Clinvar id is 6550.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-189866712-G-A is described in CliVar as Pathogenic/Likely_pathogenic. Clinvar id is 6550.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-189866712-G-A is described in CliVar as Pathogenic/Likely_pathogenic. Clinvar id is 6550.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-189866712-G-A is described in CliVar as Pathogenic/Likely_pathogenic. Clinvar id is 6550.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-189866712-G-A is described in CliVar as Pathogenic/Likely_pathogenic. Clinvar id is 6550.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-189866712-G-A is described in CliVar as Pathogenic/Likely_pathogenic. Clinvar id is 6550.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-189866712-G-A is described in CliVar as Pathogenic/Likely_pathogenic. Clinvar id is 6550.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-189866712-G-A is described in CliVar as Pathogenic/Likely_pathogenic. Clinvar id is 6550.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-189866712-G-A is described in CliVar as Pathogenic/Likely_pathogenic. Clinvar id is 6550.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-189866712-G-A is described in CliVar as Pathogenic/Likely_pathogenic. Clinvar id is 6550.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-189866712-G-A is described in CliVar as Pathogenic/Likely_pathogenic. Clinvar id is 6550.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-189866712-G-A is described in CliVar as Pathogenic/Likely_pathogenic. Clinvar id is 6550.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-189866712-G-A is described in CliVar as Pathogenic/Likely_pathogenic. Clinvar id is 6550.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-189866712-G-A is described in CliVar as Pathogenic/Likely_pathogenic. Clinvar id is 6550.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-189866712-G-A is described in CliVar as Pathogenic/Likely_pathogenic. Clinvar id is 6550.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-189866712-G-A is described in CliVar as Pathogenic/Likely_pathogenic. Clinvar id is 6550.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-189866712-G-A is described in CliVar as Pathogenic/Likely_pathogenic. Clinvar id is 6550.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TP63	NM_003722.5 link	c.797G>A	p.Arg266Gln	missense_variant	Exon 6 of 14	ENST00000264731.8	NP_003713.3	Q9H3D4-1A0A0S2Z4N5
TP63	NM_001114980.2 link	c.515G>A	p.Arg172Gln	missense_variant	Exon 4 of 12	ENST00000354600.10	NP_001108452.1	Q9H3D4-2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TP63	ENST00000264731.8 link	c.797G>A	p.Arg266Gln	missense_variant	Exon 6 of 14	1	NM_003722.5	ENSP00000264731.3		Q9H3D4-1
TP63	ENST00000354600.10 link	c.515G>A	p.Arg172Gln	missense_variant	Exon 4 of 12	1	NM_001114980.2	ENSP00000346614.5		Q9H3D4-2

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

Cov.:

GnomAD4 genome

Cov.:

Alfa

AF:

0.0000516

Hom.:

ClinVar

Significance: Pathogenic/Likely pathogenic

Submissions summary: Pathogenic:8

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

Ectrodactyly, ectodermal dysplasia, and cleft lip-palate syndrome 3

Pathogenic:4

Bioscientia Institut fuer Medizinische Diagnostik GmbH, Sonic Healthcare

Significance:Pathogenic

Review Status:no assertion criteria provided

Collection Method:clinical testing

- -

Sep 18, 2023

3billion

Significance:Pathogenic

Review Status:criteria provided, single submitter

Collection Method:clinical testing

The variant is not observed in the gnomAD v2.1.1 dataset. Predicted Consequence/Location: Missense changes are a common disease-causing mechanism. In silico tool predictions suggest damaging effect of the variant on gene or gene product [REVEL: 0.84 (>=0.6, sensitivity 0.68 and specificity 0.92); 3Cnet: 0.97 (>=0.6, sensitivity 0.72 and precision 0.9)]. Same nucleotide change resulting in same amino acid change has been previously reported as pathogenic/likely pathogenic with strong evidence (ClinVar ID: VCV000006550 /PMID: 11462173). Different missense changes at the same codon (p.Arg266Leu, p.Arg266Pro) have been reported to be associated with TP63 related disorder (ClinVar ID: VCV000030348, VCV001486558 /PMID: 21204238). Therefore, this variant is classified as Pathogenic according to the recommendation of ACMG/AMP guideline. -

Apr 04, 2022

MGZ Medical Genetics Center

Significance:Likely pathogenic

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Jan 01, 2011

OMIM

Significance:Pathogenic

Review Status:no assertion criteria provided

Collection Method:literature only

- -

not provided

Pathogenic:2

Sep 16, 2018

Gharavi Laboratory, Columbia University

Significance:Pathogenic

Review Status:no assertion criteria provided

Collection Method:research

- -

Feb 24, 2025

GeneDx

Significance:Pathogenic

Review Status:criteria provided, single submitter

Collection Method:clinical testing

Published functional studies demonstrate a damaging effect as the R226Q variant enhanced transactivation and regulation of mRNA and protein targets (PMID: 18626511); Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Also known as p.R227Q; This variant is associated with the following publications: (PMID: 21204238, 23736768, 17041931, 11462173, 17431922, 26075610, 38357259, 37072394, 17224651, 21652629, 18626511) -

ADULT syndrome

Pathogenic:1

Jan 01, 2011

OMIM

Significance:Pathogenic

Review Status:no assertion criteria provided

Collection Method:literature only

- -

TP63-Related Spectrum Disorders

Pathogenic:1

Aug 07, 2022

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Pathogenic

Review Status:criteria provided, single submitter

Collection Method:clinical testing

For these reasons, this variant has been classified as Pathogenic. Experimental studies are conflicting or provide insufficient evidence to determine the effect of this variant on TP63 function (PMID: 18626511). This sequence change replaces arginine, which is basic and polar, with glutamine, which is neutral and polar, at codon 266 of the TP63 protein (p.Arg266Gln). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individual(s) with TP63-related conditions (PMID: 11462173). It has also been observed to segregate with disease in related individuals. This variant is also known as R227Q. ClinVar contains an entry for this variant (Variation ID: 6550). Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Benign"; Align-GVGD: "Class C35"). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Pathogenic

0.99

BayesDel_addAF

Pathogenic

0.54

BayesDel_noAF

Pathogenic

0.54

CADD

Pathogenic

(source)

DANN

Pathogenic

1.0

DEOGEN2

Pathogenic

0.98

D;.;.;.;.;.;.;.;.;.;.

Eigen

Uncertain

0.60

Eigen_PC

Pathogenic

0.68

FATHMM_MKL

Pathogenic

0.99

LIST_S2

Pathogenic

0.99

D;D;D;D;D;D;D;D;D;D;D

M_CAP

Pathogenic

0.53

MetaRNN

Pathogenic

0.99

D;D;D;D;D;D;D;D;D;D;D

MetaSVM

Pathogenic

1.1

MutationAssessor

Uncertain

2.0

M;M;M;M;M;.;.;.;.;.;.

PhyloP100

9.9

PrimateAI

Pathogenic

0.82

PROVEAN

Uncertain

-3.6

D;D;D;D;D;D;D;D;D;D;D

REVEL

Pathogenic

0.84

Sift

Uncertain

0.0010

D;D;D;D;D;D;D;D;D;D;D

Sift4G

Uncertain

0.025

D;D;D;D;D;D;D;D;D;D;D

Polyphen

0.79

P;D;P;D;P;P;P;P;.;P;.

Vest4

0.96

MutPred

0.97

Loss of sheet (P = 0.1158);Loss of sheet (P = 0.1158);Loss of sheet (P = 0.1158);Loss of sheet (P = 0.1158);Loss of sheet (P = 0.1158);.;.;.;.;.;.;

MVP

1.0

MPC

0.74

ClinPred

0.98

GERP RS

5.6

Varity_R

0.87

gMVP

0.93

Mutation Taster

=0/100

disease causing (ClinVar)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over