NM_004820.5(CYP7B1):c.1162C>T (p.Arg388Ter) AND Spastic paraplegia

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Sep 11, 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:: RCV000800899.9

Allele description [Variation Report for NM_004820.5(CYP7B1):c.1162C>T (p.Arg388Ter)]

NM_004820.5(CYP7B1):c.1162C>T (p.Arg388Ter)

Gene:

CYP7B1:cytochrome P450 family 7 subfamily B member 1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

8q12.3

Genomic location:

Preferred name:

NM_004820.5(CYP7B1):c.1162C>T (p.Arg388Ter)

HGVS:

NC_000008.11:g.64604753G>A
NG_008338.2:g.199039C>T
NM_001324112.2:c.1162C>T
NM_004820.5:c.1162C>TMANE SELECT
NP_001311041.1:p.Arg388Ter
NP_004811.1:p.Arg388Ter
NC_000008.10:g.65517310G>A
NM_004820.3:c.1162C>T

Protein change:

R388*; ARG388TER

Links:

OMIM: 603711.0001; dbSNP: rs72554620

NCBI 1000 Genomes Browser:

rs72554620

Molecular consequence:

NM_001324112.2:c.1162C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_004820.5:c.1162C>T - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Name:: Spastic paraplegia
Identifiers:: MedGen: C0037772; Human Phenotype Ontology: HP:0001258

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zinc finger protein 541 isoform X6 [Homo sapiens]
zinc finger protein 541 isoform X6 [Homo sapiens]
gi|768011431|ref|XP_011525676.1|

Protein
INPUT_1
INPUT_1

GEO DataSets

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000940642	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Sep 11, 2023)	germline	clinical testing	PubMed (9) [See all records that cite these PMIDs] 19363635, 19439420, 21541746, 21567895, 28039895, 9802883, 18252231, 19812052, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000940642

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Sep 11, 2023)

germline

clinical testing

PubMed (9)
[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	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Two novel CYP7B1 mutations in Italian families with SPG5: a clinical and genetic study.

Criscuolo C, Filla A, Coppola G, Rinaldi C, Carbone R, Pinto S, Wang Q, de Leva MF, Salvatore E, Banfi S, Brunetti A, Quarantelli M, Geschwind DH, Pappatà S, De Michele G.

J Neurol. 2009 Aug;256(8):1252-7. doi: 10.1007/s00415-009-5109-3. Epub 2009 Apr 12.

PubMed [citation]

PMID:: 19363635

CYP7B1 mutations in pure and complex forms of hereditary spastic paraplegia type 5.

Goizet C, Boukhris A, Durr A, Beetz C, Truchetto J, Tesson C, Tsaousidou M, Forlani S, Guyant-Maréchal L, Fontaine B, Guimarães J, Isidor B, Chazouillères O, Wendum D, Grid D, Chevy F, Chinnery PF, Coutinho P, Azulay JP, Feki I, Mochel F, Wolf C, et al.

Brain. 2009 Jun;132(Pt 6):1589-600. doi: 10.1093/brain/awp073. Epub 2009 May 12.

PubMed [citation]

PMID:: 19439420

See all PubMed Citations (9)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV000940642.6

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (9)

Description

This sequence change creates a premature translational stop signal (p.Arg388*) in the CYP7B1 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in CYP7B1 are known to be pathogenic (PMID: 9802883, 19363635, 19439420, 21541746, 21567895, 28039895). This variant is present in population databases (rs72554620, gnomAD 0.005%). This premature translational stop signal has been observed in individuals with hereditary spastic paraplegia and neonatal liver failure (PMID: 9802883, 18252231, 19812052). ClinVar contains an entry for this variant (Variation ID: 6100). For these reasons, this variant has been classified as Pathogenic.

#	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

Last Updated: Oct 8, 2024

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