NM_000350.3(ABCA4):c.5461-10T>C AND Cone-rod dystrophy 3

Germline classification:: Pathogenic (3 submissions)
Last evaluated:: Aug 3, 2021
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:: RCV000008366.13

Allele description [Variation Report for NM_000350.3(ABCA4):c.5461-10T>C]

NM_000350.3(ABCA4):c.5461-10T>C

Gene:

ABCA4:ATP binding cassette subfamily A member 4 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

1p22.1

Genomic location:

Preferred name:

NM_000350.3(ABCA4):c.5461-10T>C

Other names:

NP_000341.2:p.?

HGVS:

NC_000001.11:g.94011395A>G
NG_009073.1:g.114755T>C
NG_009073.2:g.114753T>C
NG_091644.1:g.185A>G
NM_000350.3:c.5461-10T>CMANE SELECT
NC_000001.10:g.94476951A>G
NM_000350.2:c.5461-10T>C

Nucleotide change:

IVS39AS, T-C, -10

Links:

OMIM: 601691.0030; dbSNP: rs1800728

NCBI 1000 Genomes Browser:

rs1800728

Molecular consequence:

NM_000350.3:c.5461-10T>C - intron variant - [Sequence Ontology: SO:0001627]

Functional consequence:

functionally_normal [Sequence Ontology: SO:0002219]

Condition(s)

Name:: Cone-rod dystrophy 3 (CORD3)
Identifiers:: MONDO: MONDO:0011395; MedGen: C1858806; Orphanet: 1872; OMIM: 604116

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000028574	OMIM	no assertion criteria provided	Pathogenic (Jul 1, 2008)	germline	literature only	PubMed (1) [See all records that cite this PMID]
SCV000536892	Division of Human Genetics, Children's Hospital of Philadelphia - CSER-PediSeq	no assertion criteria provided	Pathogenic (Feb 23, 2016)	germline	research	PubMed (10) [See all records that cite these PMIDs] 25082885, 24713488, 20696155, 19074458, 23591405, 23695285, 10958763, 22328824, 22264887, 25097241
SCV001950069	Institute of Human Genetics, University of Leipzig Medical Center	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Aug 3, 2021)	unknown	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

SCV000028574

OMIM

no assertion criteria provided

Pathogenic
(Jul 1, 2008)

germline

literature only

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

SCV000536892

Division of Human Genetics, Children's Hospital of Philadelphia - CSER-PediSeq

no assertion criteria provided

Pathogenic
(Feb 23, 2016)

germline

research

PubMed (10)
[See all records that cite these PMIDs]

SCV001950069

Institute of Human Genetics, University of Leipzig Medical Center

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Aug 3, 2021)

unknown

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	germline	unknown	not provided	not provided	not provided	not provided	not provided	research
not provided	germline	not provided	not provided	not provided	not provided	not provided	not provided	literature only
not provided	unknown	yes	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

ABCA4 gene analysis in patients with autosomal recessive cone and cone rod dystrophies.

Kitiratschky VB, Grau T, Bernd A, Zrenner E, Jägle H, Renner AB, Kellner U, Rudolph G, Jacobson SG, Cideciyan AV, Schaich S, Kohl S, Wissinger B.

Eur J Hum Genet. 2008 Jul;16(7):812-9. doi: 10.1038/ejhg.2008.23. Epub 2008 Feb 20.

PubMed [citation]

PMID:: 18285826
PMCID:: PMC2579899

Molecular diagnostic testing by eyeGENE: analysis of patients with hereditary retinal dystrophy phenotypes involving central vision loss.

Alapati A, Goetz K, Suk J, Navani M, Al-Tarouti A, Jayasundera T, Tumminia SJ, Lee P, Ayyagari R.

Invest Ophthalmol Vis Sci. 2014 Jul 31;55(9):5510-21. doi: 10.1167/iovs.14-14359.

PubMed [citation]

PMID:: 25082885
PMCID:: PMC4152151

See all PubMed Citations (12)

Details of each submission

From OMIM, SCV000028574.2

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

Description

In 6 patients with cone-rod dystrophy (CORD3; 604116), 1 with cone dystrophy, and 1 with cone dystrophy but no information on rod function, all of whom had a family history consistent with autosomal recessive inheritance, Kitiratschky et al. (2008) identified compound heterozygosity for a splice site mutation (5461-10T-C) in intron 39 and another mutation in the ABCA4 gene (see, e.g., 601690.0001 and 601690.0007). In 2 of the CORD3 patients, a mutation on the second allele was not detected; the authors noted that with the methods used, genomic rearrangement mutations could not be excluded.

#	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 Division of Human Genetics, Children's Hospital of Philadelphia - CSER-PediSeq, SCV000536892.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	research	PubMed (10)

#	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

From Institute of Human Genetics, University of Leipzig Medical Center, SCV001950069.1

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

Description

This variant was identified as compound heterozygous with NM_000350.3:c.1822T>A.

#	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: Apr 20, 2024

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