9-72924099-G-A

Variant names:

• chr9-72924099-G-A
• NM_000689.5:c.667C>T

Variant summary

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

The NM_000689.5(ALDH1A1):​c.667C>T​(p.Pro223Ser) 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. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: ALDH1A1 NM_000689.5 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 9.57

Genes affected

ALDH1A1 (HGNC:402): (aldehyde dehydrogenase 1 family member A1) The protein encoded by this gene belongs to the aldehyde dehydrogenase family. Aldehyde dehydrogenase is the next enzyme after alcohol dehydrogenase in the major pathway of alcohol metabolism. There are two major aldehyde dehydrogenase isozymes in the liver, cytosolic and mitochondrial, which are encoded by distinct genes, and can be distinguished by their electrophoretic mobility, kinetic properties, and subcellular localization. This gene encodes the cytosolic isozyme. Studies in mice show that through its role in retinol metabolism, this gene may also be involved in the regulation of the metabolic responses to high-fat diet. [provided by RefSeq, Mar 2011]

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, 0.784

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ALDH1A1	NM_000689.5	c.667C>T	p.Pro223Ser	missense_variant	Exon 7 of 13	ENST00000297785.8	NP_000680.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ALDH1A1	ENST00000297785.8	c.667C>T	p.Pro223Ser	missense_variant	Exon 7 of 13	1	NM_000689.5	ENSP00000297785.3
ALDH1A1	ENST00000419959.5	c.667C>T	p.Pro223Ser	missense_variant	Exon 8 of 8	5		ENSP00000388026.1
ALDH1A1	ENST00000376939.5	c.667C>T	p.Pro223Ser	missense_variant	Exon 7 of 8	5		ENSP00000366138.1
ALDH1A1	ENST00000482210.5	n.629C>T		non_coding_transcript_exon_variant	Exon 7 of 7	2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 32

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Uncertain:1

Jul 21, 2021

Ambry Genetics

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.667C>T (p.P223S) alteration is located in exon 7 (coding exon 7) of the ALDH1A1 gene. This alteration results from a C to T substitution at nucleotide position 667, causing the proline (P) at amino acid position 223 to be replaced by a serine (S). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.33
BayesDel_addAF	Pathogenic	0.21	D
BayesDel_noAF	Uncertain	0.060
CADD	Pathogenic	29
DANN	Uncertain	1.0
DEOGEN2	Uncertain	0.75	D;T;T
Eigen	Uncertain	0.64
Eigen_PC	Pathogenic	0.73
FATHMM_MKL	Pathogenic	0.99	D
LIST_S2	Uncertain	0.95	D;D;D
M_CAP	Benign	0.053	D
MetaRNN	Pathogenic	0.78	D;D;D
MetaSVM	Benign	-0.42	T
MutationAssessor	Benign	0.56	N;.;.
PrimateAI	Pathogenic	0.84	D
PROVEAN	Pathogenic	-5.4	D;D;D
REVEL	Uncertain	0.52
Sift	Benign	0.16	T;T;T
Sift4G	Benign	0.46	T;T;.
Polyphen		1.0	D;.;.
Vest4		0.74
MutPred		0.49		Gain of glycosylation at P223 (P = 0.0043);Gain of glycosylation at P223 (P = 0.0043);Gain of glycosylation at P223 (P = 0.0043);
MVP		0.54
MPC		1.0
ClinPred		0.96	D
GERP RS		6.0
Varity_R		0.77
gMVP		0.83

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.050		Details are displayed if max score is > 0.2

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr9-75539015;