chrX-23379756-A-G

Position:

chrX-23379756-A-G

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2

The NM_173495.3(PTCHD1):c.517A>G(p.Ile173Val) variant causes a missense change. The variant allele was found at a frequency of 0.000311 in 1,209,297 control chromosomes in the GnomAD database, including 2 homozygotes. There are 147 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).

Frequency

Genomes: 𝑓 0.00032 ( 0 hom., 14 hem., cov: 23)

Exomes 𝑓: 0.00031 ( 2 hom. 133 hem. )

Consequence

PTCHD1
NM_173495.3 missense

Scores

Clinical Significance

Conflicting classifications of pathogenicity criteria provided, conflicting classifications U:3B:3

Conservation

PhyloP100: 5.30

Variant links:

Genes affected

PTCHD1 (HGNC:26392): (patched domain containing 1) This gene encodes a membrane protein with a patched domain. The encoded protein is similar to Drosophila proteins which act as receptors for the morphogen sonic hedgehog. Deletions in this gene, which is located on the X chromosome, are associated with intellectual disability and autism (PMID: 21091464, PMID: 20844286). [provided by RefSeq, Aug 2011]

PTCHD1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -9 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.03401667).

BP6

Variant X-23379756-A-G is Benign according to our data. Variant chrX-23379756-A-G is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 211971.We mark this variant Likely_benign, oryginal submissions are: {Benign=3, Uncertain_significance=2}. Variant chrX-23379756-A-G is described in Lovd as [Benign].

BS2

High Hemizygotes in GnomAd4 at 14 XL gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PTCHD1	NM_173495.3 linkuse as main transcript	c.517A>G	p.Ile173Val	missense_variant	2/3	ENST00000379361.5	NP_775766.2
PTCHD1	XM_011545449.4 linkuse as main transcript	c.517A>G	p.Ile173Val	missense_variant	3/4		XP_011543751.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PTCHD1	ENST00000379361.5 linkuse as main transcript	c.517A>G	p.Ile173Val	missense_variant	2/3	1	NM_173495.3	ENSP00000368666	P1	Q96NR3-1
PTCHD1	ENST00000456522.1 linkuse as main transcript	c.159-12775A>G		intron_variant		1		ENSP00000406663

Frequencies

GnomAD3 genomes

AF:

0.000324

AC:

AN:

111016

Hom.:

Cov.:

AF XY:

0.000422

AC XY:

AN XY:

33200

show subpopulations

Gnomad AFR

AF:

0.00

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000479

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000384

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000566

Gnomad OTH

AF:

0.00

GnomAD3 exomes

AF:

0.000398

AC:

AN:

183516

Hom.:

AF XY:

0.000471

AC XY:

AN XY:

67946

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.000255

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.000839

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.000586

Gnomad OTH exome

AF:

0.000441

GnomAD4 exome

AF:

0.000310

AC:

340

AN:

1098228

Hom.:

Cov.:

AF XY:

0.000366

AC XY:

133

AN XY:

363582

show subpopulations

Gnomad4 AFR exome

AF:

0.0000379

Gnomad4 AMR exome

AF:

0.000312

Gnomad4 ASJ exome

AF:

0.0000516

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.000757

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.000313

Gnomad4 OTH exome

AF:

0.000412

GnomAD4 genome

AF:

0.000324

AC:

AN:

111069

Hom.:

Cov.:

AF XY:

0.000421

AC XY:

AN XY:

33263

show subpopulations

Gnomad4 AFR

AF:

0.00

Gnomad4 AMR

AF:

0.000478

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000385

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000566

Gnomad4 OTH

AF:

0.00

Alfa

AF:

0.000449

Hom.:

Bravo

AF:

0.000298

ESP6500AA

AF:

0.00

AC:

ESP6500EA

AF:

0.000595

AC:

ExAC

AF:

0.000412

AC:

EpiCase

AF:

0.000654

EpiControl

AF:

0.00119

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Uncertain:3Benign:3

Revision: criteria provided, conflicting classifications

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Aug 01, 2024	PTCHD1: BS1, BS2 -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Feb 19, 2021	This variant is associated with the following publications: (PMID: 20844286, 23871722) -

Autism, susceptibility to, X-linked 4

Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Mendelics

May 28, 2019

- -

not specified

Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Genetic Services Laboratory, University of Chicago

Dec 29, 2014

- -

PTCHD1-related disorder

Uncertain:1

Uncertain significance, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Dec 06, 2023

The PTCHD1 c.517A>G variant is predicted to result in the amino acid substitution p.Ile173Val. This variant has been reported in at least one male patient with autism spectrum disorder/ intellectual disability and found in his unaffected mother and one of his unaffected sisters. Of note, this male patient was also heterozygous for a de novo ~1 Mb deletion encompassing the entire DPYD gene (Carter. 2010. PubMed ID: 21114665; Noor et al. 2010. PubMed ID: 20844286). In vitro experimental studies have shown that PTCHD1 protein carrying the p.Ile173Val variant is expressed at levels comparable to wild type and localizes properly to the cell membrane; however, additional experiments to assess possible impacts on protein function were not performed (Halewa et al. 2021. PubMed ID: 33856728). This variant is reported in 0.084% of alleles in individuals of South Asian descent in gnomAD. Although we suspect that this variant may be benign, the clinical significance of this variant is uncertain at this time due to the absence of conclusive functional and genetic evidence. -

Inborn genetic diseases

Benign:1

Benign, criteria provided, single submitter

clinical testing

Ambry Genetics

Apr 27, 2020

This alteration is classified as benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.086

BayesDel_addAF

Benign

-0.11

BayesDel_noAF

Uncertain

-0.020

CADD

Benign

DANN

Benign

0.95

DEOGEN2

Benign

0.21

FATHMM_MKL

Uncertain

0.92

LIST_S2

Benign

0.83

M_CAP

Benign

0.063

MetaRNN

Benign

0.034

MetaSVM

Benign

-0.48

MutationAssessor

Benign

0.14

MutationTaster

Benign

0.96

PrimateAI

Uncertain

0.68

PROVEAN

Benign

-0.50

REVEL

Uncertain

0.44

Sift

Benign

0.70

Sift4G

Benign

1.0

Polyphen

0.11

Vest4

0.099

MVP

0.88

MPC

0.55

ClinPred

0.044

GERP RS

5.1

Varity_R

0.17

gMVP

0.77

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over