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NM_001737.5(C9):c.346C>T (p.Arg116Ter) AND Complement component 9 deficiency

Germline classification:
Pathogenic (5 submissions)
Last evaluated:
Oct 9, 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:
RCV000018568.34

Allele description [Variation Report for NM_001737.5(C9):c.346C>T (p.Arg116Ter)]

NM_001737.5(C9):c.346C>T (p.Arg116Ter)

Gene:
C9:complement C9 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
5p13.1
Genomic location:
Preferred name:
NM_001737.5(C9):c.346C>T (p.Arg116Ter)
Other names:
C9, ARG95TER; R95*
HGVS:
  • NC_000005.10:g.39341276G>A
  • NG_009894.1:g.28278C>T
  • NM_001737.5:c.346C>TMANE SELECT
  • NP_001728.1:p.Arg116Ter
  • LRG_32t1:c.346C>T
  • LRG_32:g.28278C>T
  • LRG_32p1:p.Arg116Ter
  • NC_000005.9:g.39341378G>A
  • NM_001737.3:c.346C>T
Protein change:
R116*; ARG95TER
Links:
OMIM: 120940.0001; dbSNP: rs121909592
NCBI 1000 Genomes Browser:
rs121909592
Molecular consequence:
  • NM_001737.5:c.346C>T - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Name:
Complement component 9 deficiency (C9D)
Synonyms:
C9 deficiency
Identifiers:
MONDO: MONDO:0013445; MedGen: C3151189; OMIM: 613825

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000038850OMIM
no assertion criteria provided
Pathogenic
(Mar 1, 2003)
germlineliterature only

PubMed (4)
[See all records that cite these PMIDs]

SCV001142345Reproductive Health Research and Development, BGI Genomics
no assertion criteria provided
Pathogenic
(Jan 6, 2020)
germlinecuration

SCV002018021Revvity Omics, Revvity
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Oct 26, 2020)
germlineclinical testing

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

SCV005399820Victorian Clinical Genetics Services, Murdoch Childrens Research Institute

See additional submitters

criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Oct 9, 2024)
germlineclinical testing

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

SCV005417812Juno Genomics, Hangzhou Juno Genomics, Inc
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenicgermlineclinical testing

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

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing
not providedgermlinenot providednot providednot providednot providednot providednot providedliterature only
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing, curation

Citations

PubMed

Nonsense mutation in exon 4 of human complement C9 gene is the major cause of Japanese complement C9 deficiency.

Kira R, Ihara K, Takada H, Gondo K, Hara T.

Hum Genet. 1998 Jun;102(6):605-10.

PubMed [citation]
PMID:
9703418

Hereditary complement (C9) deficiency associated with dermatomyositis.

Ichikawa E, Furuta J, Kawachi Y, Imakado S, Otsuka F.

Br J Dermatol. 2001 May;144(5):1080-3.

PubMed [citation]
PMID:
11359403
See all PubMed Citations (5)

Details of each submission

From OMIM, SCV000038850.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature only PubMed (4)

Description

Horiuchi et al. (1998) found that 8 of 10 unrelated Japanese subjects with C9 deficiency (613825) were homozygous for a C-to-T transition at nucleotide 343, which converted codon 95 from CGA (arg) to TGA (stop). Two other patients were heterozygous for the R95X mutation; one of these had a C507Y (120940.0005) substitution, while the genetic defect in the other allele of the second heterozygote remained unknown. Kira et al. (1998) likewise found that all 4 Japanese C9-deficient patients who had suffered from meningococcal meningitis had this CGA (arg)-to-TGA (stop) mutation.

Ichikawa et al. (2001) found this mutation in a 28-year-old Japanese woman with C9 deficiency and dermatomyositis. Whereas levels of serum hemolytic complement (CH50) are characteristically normal or elevated in patients with dermatomyositis, this patient showed markedly depressed levels of CH50. This case demonstrated that the muscle lesions of dermatomyositis can occur in the presence of a complement defect that would prevent the formation of the C5b-9 membrane attack complex.

The R95X mutation is responsible for most Japanese C9 deficiency cases, with a carrier frequency of 6.7%. Khajoee et al. (2003) showed that in Koreans and Chinese, the R95X carrier frequencies were 2.0% and 1.0%, respectively. The founder effect found in East Asians (Japanese, Koreans, and Chinese) but not in Caucasians, as well as the haplotype sharing in only a small chromosomal region, suggested that the R95X mutation is ancient and occurred after the divergence of East Asians and Caucasians, and before migration of the Yayoi people to Japan. Because the mortality of meningococcal infections in complement-deficient patients is lower than that in normal individuals, a founder effect and a selective advantage in isolation might be the main reasons for the high frequency of the R95X mutation in Japan.

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

From Reproductive Health Research and Development, BGI Genomics, SCV001142345.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedcurationnot provided

Description

NM_001737.3:c.346C>T in the C9 gene has an allele frequency of 0.01 in East Asian subpopulation in the gnomAD database. The C9 c.346C>T (p.Arg116*) variant has been reported in five Japanese C9-deficient patients in homozygous states (PMID: 9703418; 11359403). Another study revealed that eight of the 10 C9D subjects were homozygous for this variant, which was assumed to be a founder mutation in Japanese (PMID: 9570574). This variant is predicted to cause loss of normal protein function either through protein truncation or nonsense-mediated mRNA decay. Taken together, we interprete this variant as Pathogenic/Likely pathogenic. ACMG/AMP Criteria applied: PVS1; PM3; PS4.

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

From Revvity Omics, Revvity, SCV002018021.3

#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 Victorian Clinical Genetics Services, Murdoch Childrens Research Institute, SCV005399820.1

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

Description

Based on the classification scheme VCGS_Germline_v1.3.4, this variant is classified as Pathogenic. Following criteria are met: 0102 - Loss of function is a known mechanism of disease in this gene and is associated with C9 deficiency (MIM#613825). (I) 0106 - This gene is associated with autosomal recessive disease. (I) 0201 - Variant is predicted to cause nonsense-mediated decay (NMD) and loss of protein (premature termination codon is located at least 54 nucleotides upstream of the final exon-exon junction). (SP) 0251 - This variant is heterozygous. (I) 0305 - Variant is present in gnomAD >=0.01 and <0.03 for a recessive condition (v2: 224 heterozygotes, 0 homozygotes; v3: 87 heterozygotes, 1 homozygote). (I) 0701 - Other NMD-predicted variants comparable to the one identified in this case have very strong previous evidence for pathogenicity (DECIPHER). (SP) 0801 - This variant has strong previous evidence of pathogenicity in unrelated individuals. This variant has been reported as pathogenic in multiple individuals with C9 deficiency and is regarded as a Japanese founder variant (ClinVar, PMID: 9570574). (SP) 1208 - Inheritance information for this variant is not currently available in this individual. (I) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign

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

From Juno Genomics, Hangzhou Juno Genomics, Inc, SCV005417812.1

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

Description

PVS1+PM3

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

Last Updated: Jan 26, 2025