VCV002571907.3 - ClinVar

NM_014639.4(SKIC3):c.53_54del (p.Arg18fs)

Germline

Classification

The aggregate germline classification for this variant, typically for a monogenic or Mendelian disorder as in the ACMG/AMP guidelines, or for response to a drug. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the aggregate classification.

(3)

Stars represent the aggregate review status, or the level of review supporting the aggregate germline classification for this VCV record. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. The number of submissions which contribute to this review status is shown in parentheses.

Pathogenic/Likely pathogenic

criteria provided, multiple submitters, no conflicts

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

NM_014639.4(SKIC3):c.53_54del (p.Arg18fs)

Variation ID: 2571907 Accession: VCV002571907.3

Type and length

Deletion, 2 bp

Location

Cytogenetic: 5q15 5: 95547097-95547098 (GRCh38) [ NCBI UCSC ] 5: 94882801-94882802 (GRCh37) [ NCBI UCSC ]

Timeline in ClinVar

	First in ClinVar Help The date this variant first appeared in ClinVar with each type of classification.	Last submission Help The date of the most recent submission for each type of classification for this variant.	Last evaluated Help The most recent date that a submitter evaluated this variant for each type of classification.
Germline	Jul 17, 2023	Feb 28, 2024	Aug 9, 2023

HGVS

Nucleotide	Protein	Molecular consequence
NM_014639.4:c.53_54del MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.	NP_055454.1:p.Arg18fs	frameshift
NM_014639.3:c.52_53delAG	NP_055454.1:p.Arg18Lysfs	frameshift
NC_000005.10:g.95547098_95547099del
NC_000005.9:g.94882802_94882803del
NG_023414.1:g.12908_12909del
LRG_173:g.12908_12909del
LRG_173t1:c.53_54del

... more HGVS ... less HGVS

Protein change

R18fs

Other names

Canonical SPDI

NC_000005.10:95547096:TCT:T

Functional consequence Help The effect of the variant on RNA or protein function, based on experimental evidence from submitters.

Global minor allele frequency (GMAF) Help The global minor allele frequency calculated by the 1000 Genomes Project. The minor allele at this location is indicated in parentheses and may be different from the allele represented by this VCV record.

Allele frequency Help The frequency of the allele represented by this VCV record.

Links

VarSome

Genes

Gene	OMIM	ClinGen Gene Dosage Sensitivity Curation		Variation Viewer Help Links to Variation Viewer, a genome browser to view variation data from NCBI databases.	Related variants
Gene	OMIM	HI score Help The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team.	TS score Help The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team.		Within gene Help The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants.	All Help The number of variants in ClinVar for this gene, including smaller variants within the gene and larger CNVs that overlap or fully contain the gene.
SKIC3		-	-	GRCh38 GRCh37	1344	1372

Conditions - Germline

Condition Help The condition for this variant-condition (RCV) record in ClinVar.	Classification Help The aggregate germline classification for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to this aggregate classification is shown in parentheses. (# of submissions)	Review status Help The aggregate review status for this variant-condition (RCV) record in ClinVar. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status.	Last evaluated Help The most recent date that a submitter evaluated this variant for the condition.	Variation/condition record Help The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page.
not provided	Pathogenic (2)	criteria provided, multiple submitters, no conflicts	Aug 2, 2023	RCV003313616.3
Trichohepatoenteric syndrome 1	Likely pathogenic (1)	criteria provided, single submitter	Aug 9, 2023	RCV003485868.2

Submissions - Germline

Classification Help The submitted germline classification for each SCV record. (Last evaluated)	Review status Help Stars represent the review status, or the level of review supporting the submitted (SCV) record. This value is calculated by NCBI based on data from the submitter. Read our rules for calculating the review status. This column also includes a link to the submitter’s assertion criteria if provided, and the collection method. (Assertion criteria)	Condition Help The condition for the classification, provided by the submitter for this submitted (SCV) record. This column also includes the affected status and allele origin of individuals observed with this variant.	Submitter Help The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar.	More information Help This column includes more information supporting the classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter.
Pathogenic (Jan 06, 2023)	criteria provided, single submitter (GeneDx Variant Classification Process June 2021) Method: clinical testing	Not Provided Affected status: yes Allele origin: germline	GeneDx Accession: SCV004012627.1 First in ClinVar: Jul 16, 2023 Last updated: Jul 16, 2023	Comment: Frameshift variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss of function is a known mechanism of … (more) Frameshift 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: 35366317) (less)
Likely pathogenic (Aug 09, 2023)	criteria provided, single submitter (ACMG Guidelines, 2015) Method: clinical testing	Trichohepatoenteric syndrome 1 Affected status: unknown Allele origin: germline	Revvity Omics, Revvity Accession: SCV004238778.1 First in ClinVar: Feb 04, 2024 Last updated: Feb 04, 2024
Pathogenic (Aug 02, 2023)	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015)) Method: clinical testing	not provided Affected status: unknown Allele origin: germline	Labcorp Genetics (formerly Invitae), Labcorp Accession: SCV004676576.1 First in ClinVar: Feb 28, 2024 Last updated: Feb 28, 2024	Publications: PubMed (3) PubMed: 35366317‚ 20176027‚ 21120949 Comment: For these reasons, this variant has been classified as Pathogenic. ClinVar contains an entry for this variant (Variation ID: 2571907). This premature translational stop signal … (more) For these reasons, this variant has been classified as Pathogenic. ClinVar contains an entry for this variant (Variation ID: 2571907). This premature translational stop signal has been observed in individual(s) with Trichohepatoenteric syndrome (PMID: 35366317). This variant is present in population databases (rs751870750, gnomAD 0.002%). This sequence change creates a premature translational stop signal (p.Arg18Lysfs*12) in the TTC37 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in TTC37 are known to be pathogenic (PMID: 20176027, 21120949). (less)

Comment:

Frameshift 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: 35366317)

Comment:

For these reasons, this variant has been classified as Pathogenic. ClinVar contains an entry for this variant (Variation ID: 2571907). This premature translational stop signal has been observed in individual(s) with Trichohepatoenteric syndrome (PMID: 35366317). This variant is present in population databases (rs751870750, gnomAD 0.002%). This sequence change creates a premature translational stop signal (p.Arg18Lysfs*12) in the TTC37 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in TTC37 are known to be pathogenic (PMID: 20176027, 21120949).

Germline Functional Evidence

There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Comment:

Citations for germline classification of this variant

Title	Author	Journal	Year	Link
Clinical Phenotypes and Outcomes in Monogenic Versus Non-monogenic Very Early Onset Inflammatory Bowel Disease.	Collen LV	Journal of Crohn's & colitis	2022	PMID: 35366317
Novel mutations in TTC37 associated with tricho-hepato-enteric syndrome.	Fabre A	Human mutation	2011	PMID: 21120949
Mutations in TTC37 cause trichohepatoenteric syndrome (phenotypic diarrhea of infancy).	Hartley JL	Gastroenterology	2010	PMID: 20176027

Text-mined citations for this variant ...

Record last updated Sep 30, 2024

ClinVar Genomic variation as it relates to human health

NM_014639.4(SKIC3):c.53_54del (p.Arg18fs)

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for this variant ...