chr1-18872906-G-T

Variant names:

• chr1-18872906-G-T
• rs72953172
• NM_003748.4:c.1631C>A

Variant summary

Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2 PP3

The NM_003748.4(ALDH4A1):​c.1631C>A​(p.Pro544Gln) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P544L) has been classified as Likely benign.

• Frequency: Genomes: not found (cov: 33)
• Consequence: ALDH4A1 NM_003748.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 9.74

Genes affected

ALDH4A1 (HGNC:406): (aldehyde dehydrogenase 4 family member A1) This protein belongs to the aldehyde dehydrogenase family of proteins. This enzyme is a mitochondrial matrix NAD-dependent dehydrogenase which catalyzes the second step of the proline degradation pathway, converting pyrroline-5-carboxylate to glutamate. Deficiency of this enzyme is associated with type II hyperprolinemia, an autosomal recessive disorder characterized by accumulation of delta-1-pyrroline-5-carboxylate (P5C) and proline. Alternatively spliced transcript variants encoding different isoforms have been identified for this gene. [provided by RefSeq, Jun 2009]

ACMG classification

Verdict is Uncertain_significance. Variant got 3 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.833

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ALDH4A1	NM_003748.4	c.1631C>A	p.Pro544Gln	missense_variant	Exon 15 of 15	ENST00000375341.8	NP_003739.2
ALDH4A1	NM_170726.3	c.1631C>A	p.Pro544Gln	missense_variant	Exon 15 of 16		NP_733844.1
ALDH4A1	NM_001319218.2	c.1478C>A	p.Pro493Gln	missense_variant	Exon 14 of 14		NP_001306147.1
ALDH4A1	NM_001161504.2	c.1451C>A	p.Pro484Gln	missense_variant	Exon 15 of 15		NP_001154976.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ALDH4A1	ENST00000375341.8	c.1631C>A	p.Pro544Gln	missense_variant	Exon 15 of 15	1	NM_003748.4	ENSP00000364490.3
ALDH4A1	ENST00000290597.9	c.1631C>A	p.Pro544Gln	missense_variant	Exon 15 of 16	1		ENSP00000290597.5
ALDH4A1	ENST00000538839.5	c.1478C>A	p.Pro493Gln	missense_variant	Exon 14 of 14	1		ENSP00000446071.1
ALDH4A1	ENST00000538309.5	c.1451C>A	p.Pro484Gln	missense_variant	Exon 15 of 15	2		ENSP00000442988.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Uncertain	0.52
BayesDel_addAF	Pathogenic	0.36	D
BayesDel_noAF	Pathogenic	0.28
CADD	Pathogenic	29
DANN	Uncertain	0.99
DEOGEN2	Uncertain	0.43	T;.;T;.
Eigen	Pathogenic	0.82
Eigen_PC	Pathogenic	0.77
FATHMM_MKL	Pathogenic	0.97	D
LIST_S2	Pathogenic	0.99	.;D;D;D
M_CAP	Benign	0.063	D
MetaRNN	Pathogenic	0.83	D;D;D;D
MetaSVM	Uncertain	0.22	D
MutationAssessor	Pathogenic	3.1	M;.;M;.
PrimateAI	Uncertain	0.59	T
PROVEAN	Pathogenic	-5.3	D;D;D;D
REVEL	Pathogenic	0.69
Sift	Uncertain	0.027	D;D;D;D
Sift4G	Uncertain	0.0070	D;D;D;D
Polyphen		1.0	D;.;D;.
Vest4		0.84
MutPred		0.52		Gain of MoRF binding (P = 0.0335);.;Gain of MoRF binding (P = 0.0335);.;
MVP		0.94
MPC		0.50
ClinPred		1.0	D
GERP RS		4.8
Varity_R		0.69
gMVP		0.73

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs72953172; hg19: chr1-19199400;