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NM_000288.4(PEX7):c.74C>T (p.Ser25Phe)

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Interpretation:
Conflicting interpretations of pathogenicity​

Likely pathogenic(1);Uncertain significance(1)

Review status:
criteria provided, conflicting interpretations
Submissions:
2 (Most recent: Apr 2, 2018)
Last evaluated:
Jan 3, 2018
Accession:
VCV000188918.1
Variation ID:
188918
Description:
single nucleotide variant
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NM_000288.4(PEX7):c.74C>T (p.Ser25Phe)

Allele ID
186699
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
6q23.3
Genomic location
6: 136822739 (GRCh38) GRCh38 UCSC
6: 137143877 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000006.11:g.137143877C>T
NC_000006.12:g.136822739C>T
NG_008462.1:g.5160C>T
NM_000288.4:c.74C>T MANE Select NP_000279.1:p.Ser25Phe missense
Protein change
S25F
Other names
-
Canonical SPDI
NC_000006.12:136822738:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
-
Links
ClinGen: CA274123
dbSNP: rs61753236
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Likely pathogenic 1 criteria provided, single submitter Aug 12, 2014 RCV000169280.1
Uncertain significance 1 criteria provided, single submitter Jan 3, 2018 RCV000654914.1
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
PEX7 - - GRCh38
GRCh37
291 310

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely pathogenic
(Aug 12, 2014)
criteria provided, single submitter
Method: literature only
Rhizomelic chondrodysplasia punctata type 1
(Autosomal recessive inheritance)
Allele origin: unknown
Counsyl
Accession: SCV000220587.1
Submitted: (Mar 11, 2015)
Evidence details
Publications
PubMed (2)
Uncertain significance
(Jan 03, 2018)
criteria provided, single submitter
Method: clinical testing
Peroxisome biogenesis disorder 9B
Allele origin: germline
Invitae
Accession: SCV000776818.1
Submitted: (Apr 02, 2018)
Evidence details
Publications
PubMed (1)
Comment:
This sequence change replaces serine with phenylalanine at codon 25 of the PEX7 protein (p.Ser25Phe). The serine residue is highly conserved and there is a … (more)

Functional evidence

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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.

Citations for this variant

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Title Author Journal Year Link
Using whole-exome sequencing to identify inherited causes of autism. Yu TW Neuron 2013 PMID: 23352163
Mutation analysis of PEX7 in 60 probands with rhizomelic chondrodysplasia punctata and functional correlations of genotype with phenotype. Braverman N Human mutation 2002 PMID: 12325024

Text-mined citations for rs61753236...

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These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Oct 08, 2021