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NM_003805.5(CRADD):c.382G>C (p.Gly128Arg) AND Intellectual disability, autosomal recessive 34

Germline classification:
Pathogenic (3 submissions)
Last evaluated:
Dec 5, 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:
RCV000023305.9

Allele description [Variation Report for NM_003805.5(CRADD):c.382G>C (p.Gly128Arg)]

NM_003805.5(CRADD):c.382G>C (p.Gly128Arg)

Gene:
CRADD:CASP2 and RIPK1 domain containing adaptor with death domain [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
12q22
Genomic location:
Preferred name:
NM_003805.5(CRADD):c.382G>C (p.Gly128Arg)
Other names:
CRADD, GLY128ARG (rs387906861)
HGVS:
  • NC_000012.12:g.93850053G>C
  • NG_032159.2:g.177679G>C
  • NM_001320099.2:c.382G>C
  • NM_001320100.2:c.299-43997G>C
  • NM_003805.3:c.382G>C
  • NM_003805.5:c.382G>CMANE SELECT
  • NP_001307028.1:p.Gly128Arg
  • NP_003796.1:p.Gly128Arg
  • NC_000012.11:g.94243829G>C
  • NM_003805.4:c.382G>C
  • NM_003805.5:c.382G>C
  • P78560:p.Gly128Arg
Protein change:
G128R; GLY128ARG
Links:
UniProtKB: P78560#VAR_067536; OMIM: 603454.0001; dbSNP: rs387906861
NCBI 1000 Genomes Browser:
rs387906861
Molecular consequence:
  • NM_001320100.2:c.299-43997G>C - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001320099.2:c.382G>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_003805.5:c.382G>C - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Intellectual disability, autosomal recessive 34 (MRT34)
Synonyms:
INTELLECTUAL DEVELOPMENTAL DISORDER, AUTOSOMAL RECESSIVE 34, WITH VARIANT LISSENCEPHALY
Identifiers:
MONDO: MONDO:0013785; MedGen: C3281044; Orphanet: 88616; OMIM: 614499

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000044596OMIM
no assertion criteria provided
Pathogenic
(Jan 1, 2012)
germlineliterature only

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

Puffenberger, E. G. Personal Communication. 2012. Strasburg, Pa.,

SCV004241854Women's Health and Genetics/Laboratory Corporation of America, LabCorp
criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)
Pathogenic
(Dec 5, 2023)
germlineclinical testing

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

Citation Link

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlinenot providednot providednot providednot providednot providednot providedliterature only
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical 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

Genetic mapping and exome sequencing identify variants associated with five novel diseases.

Puffenberger EG, Jinks RN, Sougnez C, Cibulskis K, Willert RA, Achilly NP, Cassidy RP, Fiorentini CJ, Heiken KF, Lawrence JJ, Mahoney MH, Miller CJ, Nair DT, Politi KA, Worcester KN, Setton RA, Dipiazza R, Sherman EA, Eastman JT, Francklyn C, Robey-Bond S, Rider NL, et al.

PLoS One. 2012;7(1):e28936. doi: 10.1371/journal.pone.0028936. Epub 2012 Jan 17.

PubMed [citation]
PMID:
22279524
PMCID:
PMC3260153
See all PubMed Citations (3)

Details of each submission

From OMIM, SCV000044596.4

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

Description

In 5 Mennonite patients with autosomal recessive intellectual developmental disorder-34 with variant lissencephaly (MRT34; 614499), Puffenberger et al. (2012) identified a homozygous 382G-C transversion in the CRADD gene, resulting in a gly128-to-arg (G128R) substitution in a highly conserved residue in the CRADD death domain. The mutation was found by homozygosity mapping followed by exome sequencing. Seven heterozygous carriers of this mutation were found among 203 Mennonite control samples, yielding a population-specific allele frequency of 1.72%. (Puffenberger (2012) stated that the correct population-specific allele frequency data appear in Table 4; corresponding data in the text are incorrect.) Overexpression of mutant murine Cradd with the G128R mutation showed normal protein localization to the nucleus and cytoplasm. However, when co-overexpressed with wildtype Pidd (605247), mutant G128R Cradd formed large cytoplasmic aggregates with a relative loss of Cradd expression in the nucleus. The findings suggested that the G128R mutation alters 1 of the interaction surfaces of the CRADD death domain to decrease affinity for the PIDD death domain.

In 2 Mennonite sisters (family LR04-101) with MRT34 with thin lissencephaly, Di Donato et al. (2016) identified homozygosity for the same c.382G-C transversion (rs387906861) in the CRADD gene that had been identified in a Mennonite family (LR15-293) by Puffenberger et al. (2012). The mutation, which was found by whole-exome sequencing, was present at a low frequency in the ExAC database (0.000008).

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

From Revvity Omics, Revvity, SCV003829987.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV004241854.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (2)

Description

Variant summary: CRADD c.382G>C (p.Gly128Arg) results in a non-conservative amino acid change located in the Death domain (IPR000488) of the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 8e-06 in 251410 control chromosomes. c.382G>C has been reported in the literature in multiple homozygous individuals affected with non-syndromic intellectual disability (e.g. Puffenberger_2012) including thin lissencephaly (e.g. DiDonato_2016). These data indicate that the variant is very likely to be associated with disease. One publication reports experimental evidence showing the variant failed to activate caspase-2-initiated apoptosis required for neuronal pruning, compared to WT in vitro, however, additional evidence is necessary to make any conclusions about its effect on disease course (e.g. DiDonato_2016). The following publications have been ascertained in the context of this evaluation (PMID: 27773430, 22279524). Two submitters have cited clinical-significance assessments for this variant to ClinVar after 2014. One submitter classified the variant as pathogenic, and one submitter classified the variant as uncertain significance. Based on the evidence outlined above, the variant was classified as pathogenic.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Flagged submissions

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV003829987Revvity Omics, Revvity
flagged submission
Reason: Outlier claim with insufficient supporting evidence
Notes: None

(ACMG Guidelines, 2015)
Uncertain significance
(Jan 17, 2019)
germlineclinical testing

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

Last Updated: Jul 23, 2024