NM_138477.4(CDAN1):c.3389C>T (p.Pro1130Leu) AND not provided

This record was updated by the submitter. Please see the current version.

Germline classification:: Pathogenic/Likely pathogenic (3 submissions)
Last evaluated:: Jun 23, 2022
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:: RCV001267935.7

Allele description

NM_138477.4(CDAN1):c.3389C>T (p.Pro1130Leu)

Gene:

CDAN1:codanin 1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

15q15.2

Genomic location:

Preferred name:

NM_138477.4(CDAN1):c.3389C>T (p.Pro1130Leu)

Other names:

P1129L

HGVS:

NC_000015.10:g.42725550G>A
NG_012491.1:g.16670C>T
NM_138477.4:c.3389C>TMANE SELECT
NP_612486.2:p.Pro1130Leu
LRG_1164t1:c.3389C>T
LRG_1164:g.16670C>T
LRG_1164p1:p.Pro1130Leu
NC_000015.9:g.43017748G>A
NM_138477.2:c.3389C>T
Q8IWY9:p.Pro1130Leu

Protein change:

P1130L; PRO1129LEU

Links:

UniProtKB: Q8IWY9#VAR_017226; OMIM: 607465.0002; dbSNP: rs80338699

NCBI 1000 Genomes Browser:

rs80338699

Molecular consequence:

NM_138477.4:c.3389C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001446452	Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Oct 23, 2020)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV002573755	Mayo Clinic Laboratories, Mayo Clinic	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Oct 26, 2021)	germline	clinical testing	PubMed (10) [See all records that cite these PMIDs] 12434312, 24196372, 28102861, 28755517, 29031773, 29676459, 29936674, 30836435, 33401150, 25741868
SCV003443459	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Jun 23, 2022)	germline	clinical testing	PubMed (6) [See all records that cite these PMIDs] 28102861, 29031773, 29676459, 29936674, 33401150, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001446452

Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Oct 23, 2020)

germline

clinical testing

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

SCV002573755

Mayo Clinic Laboratories, Mayo Clinic

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
(Oct 26, 2021)

germline

clinical testing

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

SCV003443459

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Jun 23, 2022)

germline

clinical testing

PubMed (6)
[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	yes	not provided	not provided	not provided	1	not provided	clinical testing
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Congenital dyserythropoietic anemia type I is caused by mutations in codanin-1.

Dgany O, Avidan N, Delaunay J, Krasnov T, Shalmon L, Shalev H, Eidelitz-Markus T, Kapelushnik J, Cattan D, Pariente A, Tulliez M, Crétien A, Schischmanoff PO, Iolascon A, Fibach E, Koren A, Rössler J, Le Merrer M, Yaniv I, Zaizov R, Ben-Asher E, Olender T, et al.

Am J Hum Genet. 2002 Dec;71(6):1467-74. Epub 2002 Nov 14.

PubMed [citation]

PMID:: 12434312
PMCID:: PMC378595

Congenital dyserythropoietic anemia in China: a case report from two families and a review.

Ru Y, Liu G, Bai J, Dong S, Nie N, Zhang H, Zhao S, Zheng Y, Zhu X, Nie G, Zhang F, Eyden B.

Ann Hematol. 2014 May;93(5):773-7. doi: 10.1007/s00277-013-1933-8. Epub 2013 Nov 7. Review.

PubMed [citation]

PMID:: 24196372

See all PubMed Citations (11)

Details of each submission

From Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen, SCV001446452.1

#	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	germline	yes	1	not provided	not provided		not provided	not provided	not provided	not provided

From Mayo Clinic Laboratories, Mayo Clinic, SCV002573755.1

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

Description

PP3, PM2, PM3, PS4

#	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 Invitae, SCV003443459.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (6)

Description

This variant is present in population databases (rs80338699, gnomAD 0.006%). This sequence change replaces proline, which is neutral and non-polar, with leucine, which is neutral and non-polar, at codon 1130 of the CDAN1 protein (p.Pro1130Leu). For these reasons, this variant has been classified as Pathogenic. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Tolerated"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C0"). ClinVar contains an entry for this variant (Variation ID: 3177). This missense change has been observed in individual(s) with clinical features of congenital dyserythropoietic anemia (PMID: 28102861, 29031773, 29676459, 29936674, 33401150). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant.

#	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: Mar 16, 2024

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