chr9-95485866-G-A

Variant names:

• chr9-95485866-G-A
• rs1131690986
• ENST00000429896.6:c.-51C>T

Variant summary

Our verdict is Pathogenic. The variant received 14 ACMG points: 14P and 0B. PM2 PP3_Strong PP5_Very_Strong

The ENST00000429896.6(PTCH1):​c.-51C>T variant causes a 5 prime UTR premature start codon gain change. 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 Pathogenic (★★).

• Frequency: Genomes: not found (cov: 33)
• Consequence: PTCH1 ENST00000429896.6 5_prime_UTR_premature_start_codon_gain
• Clinical Significance: Pathogenic criteria provided, multiple submitters, no conflicts P:3
• Conservation: PhyloP100: 5.01
• Publications: 13 publications found

Genes affected

PTCH1 (HGNC:9585): (patched 1) This gene encodes a member of the patched family of proteins and a component of the hedgehog signaling pathway. Hedgehog signaling is important in embryonic development and tumorigenesis. The encoded protein is the receptor for the secreted hedgehog ligands, which include sonic hedgehog, indian hedgehog and desert hedgehog. Following binding by one of the hedgehog ligands, the encoded protein is trafficked away from the primary cilium, relieving inhibition of the G-protein-coupled receptor smoothened, which results in activation of downstream signaling. Mutations of this gene have been associated with basal cell nevus syndrome and holoprosencephaly. [provided by RefSeq, Aug 2017]

PTCH1 Gene-Disease associations (from GenCC):

• basal cell nevus syndrome 1

  Inheritance: AD Classification: DEFINITIVE Submitted by: G2P
• holoprosencephaly 7

  Inheritance: AD Classification: DEFINITIVE, LIMITED Submitted by: Ambry Genetics, Labcorp Genetics (formerly Invitae), G2P
• nevoid basal cell carcinoma syndrome

  Inheritance: AD Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Genomics England PanelApp, ClinGen, Labcorp Genetics (formerly Invitae), Orphanet
• holoprosencephaly

  Inheritance: AD Classification: LIMITED Submitted by: Illumina

ACMG classification

Our verdict: Pathogenic. The variant received 14 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PP3: BayesDel_addAF computational evidence supports a deleterious effect, 0.607
• PP5: Variant 9-95485866-G-A is Pathogenic according to our data. Variant chr9-95485866-G-A is described in ClinVar as Pathogenic. ClinVar VariationId is 428839.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000429896.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PTCH1	NM_000264.5	MANE Select	c.403C>T	p.Arg135*	stop_gained	Exon 3 of 24	NP_000255.2
	PTCH1	NM_001083603.3	MANE Plus Clinical	c.400C>T	p.Arg134*	stop_gained	Exon 3 of 24	NP_001077072.1
	PTCH1	NM_001083604.3		c.-51C>T		5_prime_UTR_premature_start_codon_gain	Exon 3 of 24	NP_001077073.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PTCH1	ENST00000429896.6	TSL:1	c.-51C>T		5_prime_UTR_premature_start_codon_gain	Exon 3 of 24	ENSP00000414823.2
	PTCH1	ENST00000546820.5	TSL:1	c.-51C>T		5_prime_UTR_premature_start_codon_gain	Exon 3 of 7	ENSP00000448843.1
	PTCH1	ENST00000547672.5	TSL:1	c.-51C>T		5_prime_UTR_premature_start_codon_gain	Exon 3 of 7	ENSP00000447878.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 33

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:3

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Gorlin syndrome Pathogenic:1

Nov 15, 2024

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This sequence change creates a premature translational stop signal (p.Arg135*) in the PTCH1 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in PTCH1 are known to be pathogenic (PMID: 16301862, 16419085). This variant is not present in population databases (gnomAD no frequency). This premature translational stop signal has been observed in individual(s) with basal cell nevus syndrome (PMID: 8981943, 9415689, 16508594). In at least one individual the variant was observed to be de novo. ClinVar contains an entry for this variant (Variation ID: 428839). For these reasons, this variant has been classified as Pathogenic.

not provided Pathogenic:1

Jul 26, 2022

GeneDx

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Nonsense variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss-of-function is a known mechanism of disease; Not observed at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 25525159, 18502968, 16301862, 16508594, 20690502, 30610186, 29575684, 33825892, 24204797, 33441926, 8981943)

Hereditary cancer-predisposing syndrome Pathogenic:1

Dec 12, 2022

Ambry Genetics

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The p.R135* pathogenic mutation (also known as c.403C>T), located in coding exon 3 of the PTCH1 gene, results from a C to T substitution at nucleotide position 403. This changes the amino acid from an arginine to a stop codon within coding exon 3. This mutation has previously been identified in an individual with sporadic NBCCS (Wicking C et al. Am J Hum Genet, 1997 Jan;60:21-6). This alteration is expected to result in loss of function by premature protein truncation or nonsense-mediated mRNA decay. As such, this alteration is interpreted as a disease-causing mutation.

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Pathogenic	0.61	D
BayesDel_noAF	Pathogenic	0.63
CADD	Pathogenic	41
DANN	Uncertain	1.0
Eigen	Pathogenic	0.92
Eigen_PC	Pathogenic	0.81
FATHMM_MKL	Pathogenic	0.97	D
PhyloP100		5.0
Vest4		0.98
GERP RS		5.8
Mutation Taster		=0/200	disease causing (ClinVar)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.060		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1131690986; hg19: chr9-98248148; COSMIC: COSV59462168; COSMIC: COSV59462168;