NM_153332.4(ERI1):c.464C>T (p.Pro155Leu) AND Spondyloepimetaphyseal dysplasia, Guo-Campeau type

Germline classification:: Likely pathogenic (2 submissions)
Last evaluated:: Mar 3, 2024
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:: RCV003459877.5

Allele description [Variation Report for NM_153332.4(ERI1):c.464C>T (p.Pro155Leu)]

NM_153332.4(ERI1):c.464C>T (p.Pro155Leu)

Gene:

ERI1:exoribonuclease 1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Preferred name:

NM_153332.4(ERI1):c.464C>T (p.Pro155Leu)

HGVS:

NC_000008.11:g.9011718C>T
NM_001354635.2:c.230C>T
NM_001354636.2:c.119C>T
NM_001354638.2:c.464C>T
NM_153332.4:c.464C>TMANE SELECT
NP_001341564.1:p.Pro77Leu
NP_001341565.1:p.Pro40Leu
NP_001341567.1:p.Pro155Leu
NP_699163.2:p.Pro155Leu
NC_000008.10:g.8869228C>T

Protein change:

P155L; PRO155LEU

Links:

OMIM: 608739.0005

Molecular consequence:

NM_001354635.2:c.230C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001354636.2:c.119C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001354638.2:c.464C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_153332.4:c.464C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Spondyloepimetaphyseal dysplasia, Guo-Campeau type
Synonyms:: Spondyloepimetaphyseal dysplasia, Guo-Salian type
Identifiers:: MONDO: MONDO:0958006; MedGen: C5882737; OMIM: 620663

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004190183	OMIM	no assertion criteria provided	Pathogenic (Feb 8, 2024)	germline	literature only	PubMed (1) [See all records that cite this PMID]
SCV004801357	SIB Swiss Institute of Bioinformatics	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Mar 3, 2024)	unknown	curation	PubMed (2) [See all records that cite these PMIDs] 37352860, 25741868

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004190183

OMIM

no assertion criteria provided

Pathogenic
(Feb 8, 2024)

germline

literature only

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

SCV004801357

SIB Swiss Institute of Bioinformatics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
(Mar 3, 2024)

unknown

curation

PubMed (2)
[See all records that cite these PMIDs]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	unknown	yes	not provided	not provided	not provided	not provided	not provided	curation
not provided	germline	not provided	not provided	not provided	not provided	not provided	not provided	literature only

Citations

PubMed

Null and missense mutations of ERI1 cause a recessive phenotypic dichotomy in humans.

Guo L, Salian S, Xue JY, Rath N, Rousseau J, Kim H, Ehresmann S, Moosa S, Nakagawa N, Kuroda H, Clayton-Smith J, Wang J, Wang Z, Banka S, Jackson A, Zhang YM, Wei ZJ, Hüning I, Brunet T, Ohashi H, Thomas MF, Bupp C, et al.

Am J Hum Genet. 2023 Jul 6;110(7):1068-1085. doi: 10.1016/j.ajhg.2023.06.001. Epub 2023 Jun 22.

PubMed [citation]

PMID:: 37352860
PMCID:: PMC10357479

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 OMIM, SCV004190183.4

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	literature only	PubMed (1)

Description

For discussion of the c.464C-T transition (c.464C-T, NM_153332.4) in exon 3 of the ERI1 gene, resulting in a pro155-to-leu (P155L) substitution, that was found in compound heterozygous state in 2 unrelated patients (families 2 and 4) with the Guo-Campeau type of spondyloepimetaphyseal dysplasia (SEMDGC; 620663) by Guo et al. (2023), see 608739.0004 and 608739.0006, respectively.

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

From SIB Swiss Institute of Bioinformatics, SCV004801357.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	curation	PubMed (2)

Description

This variant is interpreted for Spondyloepimetaphyseal dysplasia, Guo-Campeau type, autosomal recessive. The following ACMG Tag(s) were applied: Absent from controls (or at extremely low frequency if recessive) in gnomAD (PM2). For recessive disorders, detected in trans with a pathogenic variant (PM3). Well-established functional studies show a deleterious effect (PS3-moderate).

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

Last Updated: Jun 23, 2024

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