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NM_004715.5(CTDP1):c.863+389C>T AND Congenital cataracts-facial dysmorphism-neuropathy syndrome

Germline classification:
Pathogenic (2 submissions)
Last evaluated:
Oct 1, 2004
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of clinical impact:
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of oncogenicity:
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Record status:

Allele description [Variation Report for NM_004715.5(CTDP1):c.863+389C>T]


CTDP1:CTD phosphatase subunit 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
Genomic location:
Preferred name:
  • NC_000018.10:g.79710825C>T
  • NG_007988.1:g.36025C>T
  • NM_001202504.1:c.506+389C>T
  • NM_001318511.2:c.863+389C>T
  • NM_004715.4(CTDP1):c.863+389C>T
  • NM_004715.5:c.863+389C>TMANE SELECT
  • NM_048368.4:c.863+389C>T
  • LRG_236t1:c.863+389C>T
  • LRG_236:g.36025C>T
  • NC_000018.9:g.77470825C>T
  • NM_004715.3:c.863+389C>T
  • NM_004715.4:c.863+389C>T
Nucleotide change:
IVS6, C-T, +389
OMIM: 604927.0001; dbSNP: rs113994102
NCBI 1000 Genomes Browser:
Molecular consequence:
  • NM_001202504.1:c.506+389C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001318511.2:c.863+389C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_004715.5:c.863+389C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_048368.4:c.863+389C>T - intron variant - [Sequence Ontology: SO:0001627]


Congenital cataracts-facial dysmorphism-neuropathy syndrome (CCFDN)
CATARACT, CONGENITAL, WITH FACIAL DYSMORPHISM AND NEUROPATHY; Congenital Cataracts, Facial Dysmorphism, and Neuropathy
MONDO: MONDO:0011402; MedGen: C1858726; Orphanet: 48431; OMIM: 604168

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
no assertion criteria provided
(Oct 1, 2004)
germlineliterature only

PubMed (2)
[See all records that cite these PMIDs]

no classification provided
not providedunknownliterature only

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

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedunknownnot providednot providednot providednot providednot providednot providedliterature only
not providedgermlinenot providednot providednot providednot providednot providednot providedliterature only



Partial deficiency of the C-terminal-domain phosphatase of RNA polymerase II is associated with congenital cataracts facial dysmorphism neuropathy syndrome.

Varon R, Gooding R, Steglich C, Marns L, Tang H, Angelicheva D, Yong KK, Ambrugger P, Reinhold A, Morar B, Baas F, Kwa M, Tournev I, Guerguelcheva V, Kremensky I, Lochmüller H, Müllner-Eidenböck A, Merlini L, Neumann L, Bürger J, Walter M, Swoboda K, et al.

Nat Genet. 2003 Oct;35(2):185-9. Epub 2003 Sep 21.

PubMed [citation]

Mutation history of the roma/gypsies.

Morar B, Gresham D, Angelicheva D, Tournev I, Gooding R, Guergueltcheva V, Schmidt C, Abicht A, Lochmuller H, Tordai A, Kalmar L, Nagy M, Karcagi V, Jeanpierre M, Herczegfalvi A, Beeson D, Venkataraman V, Warwick Carter K, Reeve J, de Pablo R, Kucinskas V, Kalaydjieva L.

Am J Hum Genet. 2004 Oct;75(4):596-609. Epub 2004 Aug 20.

PubMed [citation]
See all PubMed Citations (3)

Details of each submission

From OMIM, SCV000025804.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature only PubMed (2)


In Rudari Vlax Roma (Gypsies) with congenital cataracts with facial dysmorphism and neuropathy (CCFDN; 604168), Varon et al. (2003) found perfect segregation of the disease phenotype with a C-to-T transition in an antisense Alu element in intron 6 of the CTDP1 gene (IVS6+389C-T). Screening of 887 unaffected population controls found a 6.9% carrier rate among the Rudari, in close agreement with predictions based on CCFDN prevalence; an average carrier rate of 0.6% in other Gypsy populations; and a rate of 0.0% among non-Gypsy Europeans. RT-PCR and sequencing analysis identified a rare mechanism of aberrant splicing in which the donor site created by the C-T transition activates an upstream cryptic acceptor site, resulting in the insertion of 95 nucleotides of the Alu sequence in the processed CTDP1 mRNA. This mechanism had been identified previously only in ornithine aminotransferase deficiency (258870.0023). The insertion in the CTDP1 mRNA results in a premature termination signal 17 codons downstream of exon 6, with the mutant transcript expected to undergo nonsense-mediated decay or lead to a nonfunctional protein lacking the nuclear localization signal. Varon et al. (2003) observed an abnormal product in all cell types studied, regardless of their involvement in the clinical phenotype.

Morar et al. (2004) used the IVS6+389C-T mutation and 4 other private mutations among the Roma (Gypsies) to infer some of the missing parameters relevant to the comprehensive characterization of the population history of the Gypsies. Sharing of mutations and high carrier rates supported a strong founder effect.

OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlinenot providednot providednot providednot providednot providednot providednot providednot provided

From GeneReviews, SCV000041120.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature only PubMed (1)
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownnot providednot providednot providedAssert pathogenicitynot providednot providednot providednot provided

Last Updated: May 12, 2024