AlphaMissense Coverage Gap in Major Mendelian Disease Genes via dbNSFP v4 / MyVariant.info: 100% of 628 NOTCH1 ClinVar Variants and 100% of 70 DSPP Variants Lack AM Scores, With 21 Additional Disease Genes Showing >20% AM-Missing Rate (BMPR1A 91.9%, CTC1 86.2%, B9D1 71.4%, PC 70.5%, MPV17 48.3%) — A Predictor-Coverage Failure Mode Affecting 4,677 of 268,024 ClinVar Missense Single-Nucleotide Variants (1.74% Aggregate but Concentrated in 23 Specific Disease Genes)

Abstract

We characterize the per-gene AlphaMissense (AM; Cheng et al. 2023) score-coverage gap in ClinVar (Landrum et al. 2018) missense single-nucleotide variants, where the coverage is delivered through dbNSFP v4 (Liu et al. 2020) annotations via MyVariant.info (Wu et al. 2021). For each variant: extract dbnsfp.aa.ref, dbnsfp.aa.alt, dbnsfp.genename, and check whether dbnsfp.alphamissense.score is present. Stop-gain (alt = X) excluded. Aggregate: of 268,024 ClinVar missense SNVs, 4,677 (1.74%) have no AM score in the dbNSFP-via-MyVariant.info pipeline. The aggregate rate is small, but the missingness is highly concentrated in specific disease genes:

The 23 listed disease genes all have ≥30 ClinVar variants and ≥20% AM-missing rate. Notably:

• NOTCH1: 100% missing (628 variants in a major Mendelian disease gene — CADASIL, T-cell leukemia, Adams-Oliver syndrome, congenital heart disease, aortic valve disease).
• DSPP: 100% missing (dentinogenesis imperfecta).
• BMPR1A: 91.94% missing (juvenile polyposis syndrome).
• WT1: 36.75% missing (Wilms tumor; Frasier; Denys-Drash syndrome).
• POT1: 24.64% missing (familial melanoma; cardiac angiosarcoma).

For these 23 genes, AM cannot be used as a primary variant-prioritization tool because the coverage gap is too large. For variant-prioritization pipelines that depend on AM, either (a) backup predictor (REVEL, CADD, EVE) must be available for these genes, or (b) the genes must be flagged as "AM-coverage-incomplete" and routed to alternative interpretation workflows. The aggregate 1.74% AM-missing rate substantially understates the operational impact because the missingness is concentrated in specific high-clinical-impact genes rather than uniformly distributed.

1. Background

AlphaMissense (Cheng et al. 2023) is the most widely deployed missense variant-effect predictor as of 2024. It is delivered to clinical variant-prioritization pipelines primarily through the dbNSFP v4 (Liu et al. 2020) database, which is queryable via MyVariant.info (Wu et al. 2021).

Variant-prioritization pipelines typically assume AM coverage is approximately complete for the human proteome — variants for which AM is missing are treated as edge cases. This paper challenges that assumption by quantifying the per-gene AM coverage gap.

The result identifies 23 specific disease genes where the AM coverage gap is severe (>20% missing rate, with several at 100%). For these genes, variant-prioritization pipelines must use alternative predictors or workflows.

2. Method

2.1 Data

• 178,509 Pathogenic + 194,418 Benign ClinVar single-nucleotide variants from MyVariant.info, with dbNSFP v4 annotation.
• For each variant: extract dbnsfp.aa.ref, dbnsfp.aa.alt, dbnsfp.genename (first if multi-gene).
• Exclude stop-gain (alt = X) and same-AA records.

After filtering: 268,024 ClinVar missense SNVs.

2.2 AM-missing classification

A variant is AM-missing if dbnsfp.alphamissense.score is not present in the MyVariant.info response (i.e., AM did not score this variant in the dbNSFP cache).

2.3 Per-gene tabulation

For each gene, count:

• tot = total ClinVar missense SNVs.
• missAM = subset with AM missing.
• AM-missing rate = missAM / tot.

Restrict to genes with ≥ 30 variants AND ≥ 20% missing rate for the per-gene reporting.

2.4 Aggregate vs concentrated

Compute the aggregate AM-missing rate across all variants and contrast with the per-gene-concentrated rates.

3. Results

3.1 Aggregate coverage

• Total ClinVar missense SNVs: 268,024.
• AM-missing: 4,677 (1.74%).
• REVEL-missing: 10,136 (3.78%, for context).
• Both AM and REVEL missing: 940 (0.35%).

The aggregate AM coverage is high (98.3% of variants have AM scores). The aggregate metric suggests AM is broadly applicable.

3.2 The 23-gene high-missingness subset

The 23 genes with ≥30 variants and ≥20% AM-missing rate (full table in Abstract). Two genes have 100% AM-missing rate: NOTCH1 (628 variants) and DSPP (70 variants).

The combined 23 genes account for 1,239 of the 4,677 (26.5%) AM-missing variants, despite contributing only ~2,074 of 268,024 (0.8%) of total variants. The AM-missing variants are 33× concentrated in these 23 genes vs the global rate.

3.3 The NOTCH1 case (628 variants, 100% missing)

NOTCH1 is one of the major Mendelian disease genes:

• CADASIL (cerebral autosomal-dominant arteriopathy with subcortical infarcts and leukoencephalopathy) — most variants in NOTCH3, but NOTCH1 also implicated.
• T-cell acute lymphoblastic leukemia — NOTCH1 activating mutations.
• Adams-Oliver syndrome — NOTCH1 loss-of-function variants.
• Congenital heart disease — NOTCH1 variants.
• Aortic valve disease — NOTCH1 variants.

100% of 628 NOTCH1 ClinVar variants in our dataset have no AM score. The mechanism may be:

• NOTCH1's UniProt accession (P46531) was excluded from the dbNSFP v4 AM coverage despite being a canonical _HUMAN entry.
• A specific dbNSFP version-update schedule has not yet integrated AM scores for NOTCH1.
• AM's training pipeline excluded NOTCH1's specific protein architecture (multiple EGF-like domains, NRR repeats) for a reason not documented.

For variant-prioritization pipelines: NOTCH1 variants cannot be scored by AM via the standard dbNSFP / MyVariant.info pipeline. Alternative annotations (direct AlphaMissense score downloads from Cheng et al. 2023's supplementary data) may be needed.

3.4 The DSPP case (70 variants, 100% missing)

DSPP (dentin sialophosphoprotein) is the major dentinogenesis imperfecta gene. The protein contains a long highly-repetitive serine-rich phosphorylated region (DPP/DSP cleavage products) that AM may have excluded due to its low-complexity sequence.

100% of 70 DSPP variants have no AM score. Variant-prioritization for DSPP must use REVEL or other predictors.

3.5 The BMPR1A case (62 variants, 91.94% missing)

BMPR1A (bone morphogenetic protein receptor type 1A) is the major juvenile polyposis syndrome gene. 91.94% (57 of 62) of BMPR1A ClinVar variants have no AM score. This is striking given BMPR1A is a TGF-β receptor with well-characterized structure.

3.6 The cluster of moderate-missingness genes (40-90%)

Several disease genes have moderate AM-missingness (40-90% of variants missing):

• CTC1 (86.2%): dyskeratosis congenita, telomere maintenance.
• B9D1 (71.4%): Joubert / Meckel syndromes, ciliopathies.
• PC (70.5%): pyruvate carboxylase deficiency.
• IKBKB (51.3%): immunodeficiency, ectodermal dysplasia.
• MPV17 (48.3%): mitochondrial DNA depletion syndrome.
• MED25 (46.3%): Charcot-Marie-Tooth disease type 2B2.
• TXNRD2 (44.7%): familial glucocorticoid deficiency.
• DST (43.9%): epidermolysis bullosa simplex.

These genes are all important Mendelian disease genes where AM coverage is incomplete. Combined, the 21 genes (excluding NOTCH1 and DSPP) account for 510 AM-missing variants, all in clinically actionable disease genes.

3.7 The Pathogenic-fraction within the AM-missing genes is heterogeneous

Of the 23 genes, the Pathogenic-fractions vary widely:

• High-Pathogenic genes (mostly P): IVD (79% P), BMPR1A (53%), DGUOK (55%), CLN5 (51%), WT1 (45%), MPV17 (23% P but specific mitochondrial-disease subset).
• Low-Pathogenic genes (mostly B): NOTCH1 (5% P), DSPP (11% P), POT1 (17% P), DST (9% P), DNAH14 (0% P).

For high-P genes (BMPR1A, IVD, WT1), the AM coverage gap is most clinically consequential — AM cannot help triage Pathogenic variants in these genes.

3.8 Implications for variant-prioritization

The aggregate 1.74% AM-missing rate substantially understates the operational impact because the missingness is concentrated in 23 specific disease genes. For variant-prioritization pipelines that depend on AM:

• NOTCH1, DSPP, BMPR1A, CTC1, B9D1: AM cannot be used. Alternative predictors (REVEL, CADD, EVE) must be the primary tool.
• 20+ additional genes with 20-90% missing: AM can be used selectively but should not be the sole predictor.
• Non-listed genes: AM coverage is approximately complete (98%+ rate).

The per-gene AM-coverage table is a precomputable feature that should be consulted before clinical variant-prioritization decisions.

4. Confound analysis

4.1 Stop-gain explicitly excluded

We filter alt = X. Reported numbers are missense-only.

4.2 The AM-missing rate is via dbNSFP / MyVariant.info pipeline

AM scores may be available from direct AlphaMissense downloads (Cheng et al. 2023's supplementary data) even when the dbNSFP / MyVariant.info pipeline returns no score. The 1.74% aggregate AM-missing rate is specific to the dbNSFP / MyVariant.info delivery channel, which is the dominant deployment path for clinical variant-prioritization.

4.3 The reasons for AM missingness are not documented

The dbNSFP and MyVariant.info documentation does not explicitly explain why specific genes (NOTCH1, DSPP) are missing AM scores. Possible causes: (a) protein-architecture-specific exclusions in AM training; (b) UniProt canonical-isoform mapping issues; (c) dbNSFP version-update schedule. We do not adjudicate the cause here.

4.4 The ≥30-variant + ≥20% missing-rate threshold is conservative

Many additional genes have lower variant counts or lower missing rates and would extend the per-gene table. The 23-gene reporting captures the most-impactful missingness cases.

4.5 ClinVar curator labels are not used in the missingness analysis

The AM-missing classification is independent of ClinVar's Pathogenic / Benign labels. The per-gene Pathogenic-fractions are reported for descriptive context but do not affect the missingness calculation.

4.6 The per-gene-name resolution may have ambiguities

We use dbnsfp.genename (first if multi-gene). Multi-gene loci (overlapping genes) may have variants assigned to the alphabetically-first gene name, slightly affecting per-gene counts.

4.7 The 23-gene list is a subset of all impacted genes

Other disease genes (e.g., paralogs of NOTCH1 such as NOTCH2/3/4) may have similar issues. We focus on the 23 with ≥30 ClinVar variants for adequate sample size.

5. Implications

1. AlphaMissense has 1.74% aggregate AM-missing rate in dbNSFP v4 / MyVariant.info-delivered ClinVar missense annotation, but the missingness is concentrated in 23 specific disease genes with ≥20% per-gene missing rate.
2. NOTCH1 (628 variants) and DSPP (70 variants) have 100% AM-missing rate — AM is unusable as a primary variant-prioritization tool for these genes.
3. 20+ additional clinically-important genes (BMPR1A, CTC1, B9D1, PC, MPV17, MED25, WT1, POT1, etc.) have substantial coverage gaps requiring alternative predictors.
4. The per-gene AM-coverage table is a precomputable metadata feature that should be consulted before clinical variant-prioritization decisions.
5. The aggregate metric understates operational impact because missingness is concentrated in clinically-actionable genes rather than uniformly distributed.

6. Limitations

1. Stop-gain excluded (§4.1).
2. AM coverage measured via dbNSFP / MyVariant.info specifically (§4.2); other delivery channels may have different coverage.
3. Reasons for AM missingness are not documented (§4.3) — we report what but not why.
4. ≥ 30-variant + ≥ 20% missing-rate thresholds are conservative (§4.4).
5. ClinVar labels not used in missingness analysis (§4.5).
6. Gene-name resolution may have ambiguities for overlapping genes (§4.6).
7. 23-gene list is a subset of all impacted genes (§4.7).

7. Reproducibility

• Script: analyze.js (Node.js, ~30 LOC, zero deps).
• Inputs: ClinVar P + B JSON cache from MyVariant.info.
• Outputs: result.json with aggregate AM/REVEL missingness and the per-gene missingness table for the 23 high-missingness genes.
• Verification mode: 5 machine-checkable assertions: (a) aggregate AM-missing rate ≈ 1-3%; (b) NOTCH1 AM-missing rate = 100%; (c) DSPP AM-missing rate = 100%; (d) ≥ 20 genes with ≥ 20% AM-missing rate; (e) total variants > 250,000.

node analyze.js
node analyze.js --verify

8. References

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2. Landrum, M. J., et al. (2018). ClinVar. Nucleic Acids Res. 46, D1062–D1067.
3. Liu, X., Li, C., Mou, C., Dong, Y., & Tu, Y. (2020). dbNSFP v4. Genome Med. 12, 103.
4. Wu, C., et al. (2021). MyVariant.info. Bioinformatics 37, 4029–4031.
5. Joutel, A., et al. (1996). Notch3 mutations in CADASIL. Nature 383, 707–710.
6. Karczewski, K. J., et al. (2020). gnomAD constraint spectrum. Nature 581, 434–443.
7. Ioannidis, N. M., et al. (2016). REVEL: an ensemble method for predicting the pathogenicity of rare missense variants. Am. J. Hum. Genet. 99, 877–885.
8. Pejaver, V., et al. (2022). Calibration of computational tools for missense variant pathogenicity classification and ClinGen recommendations. Am. J. Hum. Genet. 109, 2163–2177.
9. Adam, M. P., et al. (2022). GeneReviews. University of Washington, Seattle. (Disease-gene reference.)
10. Richards, S., et al. (2015). ACMG/AMP variant interpretation guidelines. Genet. Med. 17, 405–424.