NM_017775.4(TTC19):c.112C>A (p.Pro38Thr) AND not provided

Germline classification:: Uncertain significance (2 submissions)
Last evaluated:: Nov 27, 2023
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV001368703.6

Allele description [Variation Report for NM_017775.4(TTC19):c.112C>A (p.Pro38Thr)]

NM_017775.4(TTC19):c.112C>A (p.Pro38Thr)

Genes:

LOC130060311:ATAC-STARR-seq lymphoblastoid silent region 8214 [Gene]
TTC19:tetratricopeptide repeat domain 19 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

17p12

Genomic location:

Preferred name:

NM_017775.4(TTC19):c.112C>A (p.Pro38Thr)

HGVS:

NC_000017.11:g.15999960C>A
NG_029806.1:g.5581C>A
NM_001271420.2:c.-347C>A
NM_017775.4:c.112C>AMANE SELECT
NP_060245.3:p.Pro38Thr
NC_000017.10:g.15903274C>A
NM_017775.3:c.112C>A

Protein change:

P38T

Links:

dbSNP: rs962066178

NCBI 1000 Genomes Browser:

rs962066178

Molecular consequence:

NM_001271420.2:c.-347C>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_017775.4:c.112C>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Structure for Protein (Select 62739161) (6)
Structure
Profile neighbors for GEO Profiles (Select 109388642) (199)
GEO Profiles
Chromosome neighbors for GEO Profiles (Select 109435483) (19)
GEO Profiles
Brenneria tiliae strain MC1SB4.1 NODE_1_length_622534_cov_54.599155, whole genom...
Brenneria tiliae strain MC1SB4.1 NODE_1_length_622534_cov_54.599155, whole genome shotgun sequence
gi|2238916149|ref|NZ_JAKPBZ01000011 gnl|WGS:NZ_JAKPBZ01|NODE_1_length_622534_cov_54.599155

Nucleotide
IFNβ-1a in vivo treatment effect on CIS multiple sclerosis patients: peripheral ...
IFNβ-1a in vivo treatment effect on CIS multiple sclerosis patients: peripheral blood mononuclear cells
Accession: GDS4994

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001565109	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Nov 27, 2023)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV002562537	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Uncertain significance (Feb 9, 2022)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001565109

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Nov 27, 2023)

germline

clinical testing

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

SCV002562537

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Uncertain significance
(Feb 9, 2022)

germline

clinical testing

Citation Link

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
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV001565109.3

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

Description

This sequence change replaces proline, which is neutral and non-polar, with threonine, which is neutral and polar, at codon 38 of the TTC19 protein (p.Pro38Thr). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with TTC19-related conditions. ClinVar contains an entry for this variant (Variation ID: 1059427). Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Not Available"; PolyPhen-2: "Not Available"; Align-GVGD: "Not Available". The threonine amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect protein function. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

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

From GeneDx, SCV002562537.2

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

Description

In silico analysis supports that this missense variant does not alter protein structure/function; Has not been previously published as pathogenic or benign to our knowledge

#	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: Sep 29, 2024

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