NM_001379500.1(COL18A1):c.3491C>T (p.Pro1164Leu) AND Knobloch syndrome 1

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Mar 1, 2023
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV003448437.2

Allele description [Variation Report for NM_001379500.1(COL18A1):c.3491C>T (p.Pro1164Leu)]

NM_001379500.1(COL18A1):c.3491C>T (p.Pro1164Leu)

Genes:

COL18A1:collagen type XVIII alpha 1 chain [Gene - OMIM - HGNC]
SLC19A1:solute carrier family 19 member 1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

21q22.3

Genomic location:

Preferred name:

NM_001379500.1(COL18A1):c.3491C>T (p.Pro1164Leu)

HGVS:

NC_000021.9:g.45509597C>T
NG_011903.1:g.109406C>T
NG_028278.2:g.58547G>A
NM_001379500.1:c.3491C>TMANE SELECT
NM_030582.4:c.4022C>T
NM_130444.3:c.4727C>T
NP_001366429.1:p.Pro1164Leu
NP_085059.2:p.Pro1341Leu
NP_569711.2:p.Pro1576Leu
NC_000021.8:g.46929511C>T

Protein change:

P1164L

Links:

dbSNP: rs532834770

NCBI 1000 Genomes Browser:

rs532834770

Molecular consequence:

NM_001379500.1:c.3491C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_030582.4:c.4022C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_130444.3:c.4727C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Knobloch syndrome 1 (KNO1)
Identifiers:: MONDO: MONDO:0800167; MedGen: C4551775; OMIM: 267750

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004176704	Neuberg Centre For Genomic Medicine, NCGM	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Mar 1, 2023)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004176704

Neuberg Centre For Genomic Medicine, NCGM

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(Mar 1, 2023)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From Neuberg Centre For Genomic Medicine, NCGM, SCV004176704.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

Description

The missense c.3491C>T(p.Pro1164Leu) variant in COL18A1 gene has not been reported previously as a pathogenic variant nor as a benign variant, to our knowledge. The variant is reported with an allele frequency of 0.02% in the gnomAD exomes database and is novel (not in any individuals) in 1000 Genomes database. This variant has been reported to the ClinVar database as Uncertain significance. The amino acid change p.Pro1164Leu in COL18A1 is predicted as conserved by GERP++ and PhyloP across 100 vertebrates. The amino acid Pro at position 1164 is changed to a Leu changing protein sequence and it might alter its composition and physico-chemical properties. For these reasons, this variant has been classified as Variant of Uncertain Significance.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Apr 6, 2024

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