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NM_003748.4(ALDH4A1):c.1631C>T (p.Pro544Leu) AND Hyperprolinemia type 2

Germline classification:
Benign/Likely benign (2 submissions)
Last evaluated:
Jan 23, 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:
RCV000526241.12

Allele description

NM_003748.4(ALDH4A1):c.1631C>T (p.Pro544Leu)

Gene:
ALDH4A1:aldehyde dehydrogenase 4 family member A1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
1p36.13
Genomic location:
Preferred name:
NM_003748.4(ALDH4A1):c.1631C>T (p.Pro544Leu)
HGVS:
  • NC_000001.11:g.18872906G>A
  • NG_012283.1:g.34894C>T
  • NM_001161504.2:c.1451C>T
  • NM_001319218.2:c.1478C>T
  • NM_003748.4:c.1631C>TMANE SELECT
  • NM_170726.3:c.1631C>T
  • NP_001154976.1:p.Pro484Leu
  • NP_001306147.1:p.Pro493Leu
  • NP_003739.2:p.Pro544Leu
  • NP_733844.1:p.Pro544Leu
  • NC_000001.10:g.19199400G>A
  • NM_003748.3:c.1631C>T
Protein change:
P484L
Links:
dbSNP: rs72953172
NCBI 1000 Genomes Browser:
rs72953172
Molecular consequence:
  • NM_001161504.2:c.1451C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001319218.2:c.1478C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_003748.4:c.1631C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_170726.3:c.1631C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Hyperprolinemia type 2 (HYRPRO2)
Synonyms:
1-PYRROLINE-5-CARBOXYLATE DEHYDROGENASE DEFICIENCY; Delta-1-pyrroline-5-carboxylate dehydrogenase deficiency; Deficiency of pyrroline-5-carboxylate reductase
Identifiers:
MONDO: MONDO:0009401; MedGen: C2931835; Orphanet: 79101; OMIM: 239510

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000352055Illumina Laboratory Services, Illumina
criteria provided, single submitter

(ICSL Variant Classification Criteria 13 December 2019)		Likely benign
(Jan 13, 2018) 		germlineclinical testing

Citation Link,

SCV000649757Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Benign
(Jan 23, 2024) 		germlineclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
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

Details of each submission

From Illumina Laboratory Services, Illumina, SCV000352055.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease.

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

From Invitae, SCV000649757.6

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

Last Updated: Jun 17, 2024