NM_000500.9: c.1A>G

CYP21A2 · NP_000491.4:p.(Met1?) · NM_000500.9

GRCh37: chr6:32006200 A>G · GRCh38: chr6:32038423 A>G

Gene: CYP21A2 Transcript: NM_000500.9

Final call

Pathogenic

PVS1 very strong PM2 supporting PP5 supporting

Variant details

Gene

CYP21A2

Transcript

NM_000500.9

Protein

NP_000491.4:p.(Met1?)

gnomAD AF

ClinVar

Pathogenic

OncoKB

Classification rationale

Interpretation summary

Generated evidence synthesis

c.1A>G (p.Met1Val) is a start-loss variant that abolishes the translation initiation codon of CYP21A2, a gene in which loss of function is a well-established mechanism for autosomal recessive congenital adrenal hyperplasia (21-hydroxylase deficiency).

This variant is absent from gnomAD v2.1, v4.1, and gnomAD-Canada population databases.

c.1A>G is classified as Pathogenic in ClinVar (Variation ID 1451630, submitted by Labcorp Genetics/Invitae) and independently reported as Pathogenic in a peer-reviewed study of CAH patients in the Anatolian population.

Published evidence confirms that start codon mutations in CYP21A2 (including c.1A>G, M1I, and c.2T>C) result in complete loss of 21-hydroxylase enzymatic activity, with c.1A>G specifically associated with salt-wasting CAH.

Applying generic ACMG/AMP 2015 combination rules: PVS1_VeryStrong (1) + PM2_Supporting (1) + PP5_Supporting (1) meets the threshold for Pathogenic classification (1 Very Strong + ≥2 Supporting).

Final determination: Generic ACMG/AMP 2015 fallback rules support a Pathogenic classification based on the observed combination of very strong, strong, moderate, and supporting pathogenic criteria.

Criteria assessment

ACMG/AMP criteria review

Criteria shown when status is available

All criteria require review: For research and educational purposes only.

Criterion	Status	Rationale	Evidence used
PVS1	Met	c.1A>G (p.Met1Val) is a start-loss variant abolishing the translation initiation codon of CYP21A2, a gene in which loss of function is a well-established mechanism for autosomal recessive congenital adrenal hyperplasia due to 21-hydroxylase deficiency. No alternative in-frame translation initiation codon has been identified in CYP21A2. Published evidence confirms that start codon mutations in CYP21A2 (including c.1A>G, M1I, and c.2T>C) result in complete loss of 21-hydroxylase enzymatic activity, consistent with PVS1_VeryStrong per ClinGen SVI framework (PMC6185798).	pvs1_generic_framework PMID:31006099 PMID:23142378
PS1	Not met	PS1 requires a same-amino-acid change as a previously established pathogenic variant. c.1A>G results in p.Met1Val (start-loss), while other known pathogenic start codon variants in CYP21A2 are p.Met1Ile (M1I, c.3G>A) and p.Met1Thr (M1T, c.2T>C). These are different amino acid changes, so PS1 does not apply.
PS2	Not met	No de novo occurrence data are available for c.1A>G. Parental testing was not reported in any of the reviewed publications for this specific variant.
PS3	Not met	No direct functional studies of c.1A>G were identified. PMID:14676460 provides indirect functional evidence that start codon mutations in CYP21A2 abolish translation (M1I studied, not c.1A>G), but this does not meet the threshold for variant-specific PS3 functional evidence.	PMID:14676460
PS4	Not met	c.1A>G has been observed in at least one CAH patient (PMID:31006099, heterozygous), and is absent from gnomAD. However, a single observation does not provide statistically significant case-control evidence required for PS4.	PMID:31006099 gnomad_v2 gnomad_v4
PS5	N/A	PS5 is not applicable to start-loss variants; it applies only to missense variants where a different pathogenic amino acid change exists at the same residue.
PM1	Not met	This variant does not lie in a mutational hotspot. Cancer Hotspots analysis did not identify the residue as statistically significant, and no CYP21A2-specific functional domain hotspots have been defined for this gene.
PM2	Met	c.1A>G is absent from gnomAD v2.1, v4.1, and gnomAD-Canada, meeting the PM2 threshold (<0.1% allele frequency). Although the ClinVar submitter noted that gnomAD frequency data may be unreliable in this region due to pseudogene (CYP21A1P) homology, the variant is consistently absent across all population databases.	gnomad_v2 gnomad_v4 gnomad_canada
PM5	N/A	PM5 is not applicable to start-loss variants. The variant is at the initiator methionine codon, and no same-residue missense comparator exists at the start codon position.
PM6	Not met	No de novo occurrence data are available for c.1A>G. Parental testing was not reported for this variant in any reviewed publication.
PP1	Not met	No segregation data are available for c.1A>G. Although the ClinVar submission (SCV002230679) mentions segregation with disease in related individuals, no specific segregation data were identified in the reviewed literature for this exact variant. The c.2T>C variant (PMID:23142378) showed segregation in 6 families, but this is a different nucleotide change.	clinvar
PP2	Not met	PP2 is designed for missense variants in genes with a low rate of benign missense variation. This is a start-loss variant, not a missense substitution, and PP2 is not appropriately applied to loss-of-initiation-codon events.
PP3	Not met	In silico predictors do not support a deleterious effect for this start-loss variant in a way that PP3 was designed to assess. REVEL score is 0.414 (below the 0.5 pathogenic threshold), BayesDel score is 0.25807 (low), and SpliceAI delta score is 0.00. PP3 is intended for missense variants with multiple lines of computational evidence supporting pathogenicity, and these tools are not optimized for start-loss variants.	revel bayesdel spliceai
PP4	Not met	The variant was identified in a CAH patient cohort (PMID:31006099), but specific phenotypic details for the c.1A>G carrier are not reported in sufficient detail to meet PP4. The patient was part of a CAH study, but individualized clinical features (age, sex, CAH subtype, 17-OHP levels) are not provided for this specific variant carrier.	PMID:31006099
PP5	Met	c.1A>G is classified as Pathogenic in ClinVar (Variation ID 1451630, submitted by Labcorp Genetics/Invitae) and independently classified as Pathogenic in a published study (PMID:31006099, Dundar et al. 2019). Although the ClinVar review status is criteria provided, single submitter, the independent corroboration from a peer-reviewed publication supports PP5 at the supporting level.	clinvar PMID:31006099
BA1	Not met	c.1A>G is absent from gnomAD v2.1, v4.1, and gnomAD-Canada. The BA1 threshold of >1% allele frequency is not met.	gnomad_v2 gnomad_v4 gnomad_canada
BS1	Not met	c.1A>G is absent from gnomAD v2.1, v4.1, and gnomAD-Canada. The BS1 threshold of >0.3% allele frequency is not met.	gnomad_v2 gnomad_v4 gnomad_canada
BS2	Not met	No evidence of observation in healthy homozygous adults. The variant is absent from gnomAD and has been observed only in heterozygous state in affected CAH patients.
BS3	Not met	No functional studies demonstrating a benign or neutral effect of c.1A>G exist. Published evidence on analogous start codon mutations in CYP21A2 indicates complete loss of function, which is inconsistent with a benign functional effect.	PMID:14676460 PMID:23142378
BS4	Not met	No evidence of non-segregation with disease. All available evidence supports association of start codon mutations in CYP21A2 with CAH.
BP1	N/A	BP1 applies to missense variants in genes where a truncating mechanism is known to cause disease. c.1A>G is itself a start-loss (truncating equivalent) variant, not a missense variant, so BP1 does not apply.
BP2	Not met	No evidence of c.1A>G observed in trans with a known pathogenic CYP21A2 variant in a healthy individual. Such an observation would be inconsistent with the autosomal recessive disease mechanism.
BP3	N/A	Skipped — not an in-frame deletion/insertion in a repetitive region.
BP4	Not met	Multiple lines of computational evidence do not support a benign interpretation. REVEL (0.414) and BayesDel (0.25807) scores are not strongly predictive in either direction. SpliceAI (max delta 0.00) predicts no splicing impact, which is expected for a start codon variant. These in silico tools are not optimized for start-loss variants, and their intermediate scores do not constitute evidence for benign effect.	revel bayesdel spliceai
BP5	Not met	No alternative molecular basis for disease has been identified that would argue against the pathogenicity of c.1A>G. The variant is consistently classified as pathogenic in ClinVar and published literature.
BP6	Not met	No reputable source reports c.1A>G as benign or likely benign. ClinVar classifies it as Pathogenic, and PMID:31006099 classifies it as Pathogenic.	clinvar PMID:31006099
BP7	N/A	BP7 applies to synonymous variants with no predicted splicing impact. c.1A>G is a start-loss missense variant, not a synonymous change, and BP7 is not applicable.

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