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NM_000036.3(AMPD1):c.143C>T (p.Pro48Leu) AND Muscle AMP deaminase deficiency

Germline classification:
Benign (3 submissions)
Last evaluated:
Feb 1, 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:
RCV001514920.18

Allele description [Variation Report for NM_000036.3(AMPD1):c.143C>T (p.Pro48Leu)]

NM_000036.3(AMPD1):c.143C>T (p.Pro48Leu)

Gene:
AMPD1:adenosine monophosphate deaminase 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
1p13.2
Genomic location:
Preferred name:
NM_000036.3(AMPD1):c.143C>T (p.Pro48Leu)
HGVS:
  • NC_000001.11:g.114688633G>A
  • NG_008012.1:g.11923C>T
  • NM_000036.3:c.143C>TMANE SELECT
  • NM_001172626.2:c.131C>T
  • NP_000027.2:p.Pro81Leu
  • NP_000027.2:p.Pro81Leu
  • NP_000027.3:p.Pro48Leu
  • NP_001166097.2:p.Pro44Leu
  • NC_000001.10:g.115231254G>A
  • NM_000036.2:c.242C>T
Note:
NCBI staff reviewed the sequence information reported in PubMed 1631143 to determine the location of this allele on current reference sequence.
Protein change:
P44L
Links:
dbSNP: rs61752479
NCBI 1000 Genomes Browser:
rs61752479
Molecular consequence:
  • NM_000036.3:c.143C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001172626.2:c.131C>T - missense variant - [Sequence Ontology: SO:0001583]
Observations:
1

Condition(s)

Name:
Muscle AMP deaminase deficiency (MMDD)
Synonyms:
Myoadenylate deaminase deficiency, myopathy due to; Adenosine monophosphate deaminase 1 deficiency; AMP deaminase 1 deficiency; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0014220; MedGen: C3714933; Orphanet: 45; OMIM: 615511

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV001722883Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))
Benign
(Feb 1, 2024)
germlineclinical testing

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

SCV001984222Al Jalila Children’s Genomics Center, Al Jalila Childrens Speciality Hospital
criteria provided, single submitter

(ACMG Guidelines, 2015)
Benign
(Jan 6, 2020)
germlineclinical testing

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

SCV004100860Clinical Genomics Laboratory, Stanford Medicine
no assertion criteria provided
Uncertain significance
(Jan 6, 2021)
germlineclinical testing

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyes1not providednot providednot providednot providedclinical testing
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

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

Details of each submission

From Invitae, SCV001722883.4

#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 Al Jalila Children’s Genomics Center, Al Jalila Childrens Speciality Hospital, SCV001984222.1

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

From Clinical Genomics Laboratory, Stanford Medicine, SCV004100860.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
11not providednot providedclinical testingnot provided

Description

The p.Pro81Leu variant in the AMPD1 gene has been previously reported in 11 unrelated individuals with reported AMPD deficiency (Morisaki et al., 1992). Of note, all individuals were homozygous for this variant as well as the p.Gln45* variant. The highest allele frequency of the p.Pro81Leu variant was identified in the European population at 17,214/129,128 chromosomes (13.33%) by the Genome Aggregation Database (http://gnomad.broadinstitute.org/). Computational tools predict that the p.Pro81Leu variant is deleterious; however, the accuracy of in silico algorithms is limited. These data were assessed using the ACMG/AMP variant interpretation guidelines. In summary, the significance of the p.Pro81Leu variant is uncertain. Additional information is needed to resolve the significance of this variant. [ACMG evidence codes used: PP3]

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot provided1not providednot providednot provided

Last Updated: Jul 15, 2024