NM_001195553.2(DCX):c.536C>A (p.Pro179His) AND Lissencephaly type 1 due to doublecortin gene mutation

Germline classification:: Likely pathogenic (2 submissions)
Last evaluated:: Apr 5, 2024
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:: RCV003128099.2

Allele description [Variation Report for NM_001195553.2(DCX):c.536C>A (p.Pro179His)]

NM_001195553.2(DCX):c.536C>A (p.Pro179His)

Gene:

DCX:doublecortin [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

Xq23

Genomic location:

Preferred name:

NM_001195553.2(DCX):c.536C>A (p.Pro179His)

HGVS:

NC_000023.11:g.111401159G>T
NG_011750.1:g.16020C>A
NM_000555.3:c.779C>A
NM_001195553.2:c.536C>AMANE SELECT
NM_001369370.1:c.536C>A
NM_001369371.1:c.536C>A
NM_001369372.1:c.536C>A
NM_001369373.1:c.536C>A
NM_001369374.1:c.536C>A
NM_001410715.1:c.536C>A
NM_178151.3:c.536C>A
NM_178152.3:c.536C>A
NM_178153.3:c.536C>A
NP_000546.2:p.Pro260His
NP_001182482.1:p.Pro179His
NP_001356299.1:p.Pro179His
NP_001356300.1:p.Pro179His
NP_001356301.1:p.Pro179His
NP_001356302.1:p.Pro179His
NP_001356303.1:p.Pro179His
NP_001397644.1:p.Pro179His
NP_835364.1:p.Pro179His
NP_835365.1:p.Pro179His
NP_835366.1:p.Pro179His
NC_000023.10:g.110644387G>T
NM_001195553.1:c.536C>A

Protein change:

P179H

Molecular consequence:

NM_000555.3:c.779C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001195553.2:c.536C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001369370.1:c.536C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001369371.1:c.536C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001369372.1:c.536C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001369373.1:c.536C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001369374.1:c.536C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001410715.1:c.536C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_178151.3:c.536C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_178152.3:c.536C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_178153.3:c.536C>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Lissencephaly type 1 due to doublecortin gene mutation
Synonyms:: LISSENCEPHALY, X-LINKED, 1; Lissencephaly and agenesis of corpus callosum
Identifiers:: MONDO: MONDO:0010239; MedGen: C4551968; Orphanet: 2148; OMIM: 300067

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003804254	Kasturba Medical College, Manipal, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Jan 23, 2023)	de novo	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV005043028	Institute of Immunology and Genetics Kaiserslautern	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Apr 5, 2024)	de novo	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003804254

Kasturba Medical College, Manipal, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
(Jan 23, 2023)

de novo

clinical testing

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

SCV005043028

Institute of Immunology and Genetics Kaiserslautern

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
(Apr 5, 2024)

de novo

clinical testing

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

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	de novo	yes	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

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 Kasturba Medical College, Manipal, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India, SCV003804254.1

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

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

From Institute of Immunology and Genetics Kaiserslautern, SCV005043028.1

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

Description

ACMG Criteria: PM2_P, PP3, PS2, PP5; Variant was found in heterozygous state

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

Last Updated: May 26, 2024

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