# NM_144670.6(A2ML1):c.105C>T (p.Ser35=)

https://sugi.bio/variant/a2ml1-p-ser35

## Summary

**A2ML1 p.Ser35= (c.105C>T)** is classified **Benign/Likely benign** in A2ML1 (ClinVar, Multiple submitters, 4 submitters; last evaluated 2026-01-12). Ultra-rare (popmax 0.0545%, nfe).

**At a glance:** Benign/Likely benign · review: Multiple submitters · rsID rs201185025 · 4 submitters · ultra-rare (popmax 0.0545%, nfe)

## For patients & families {#patients}

This is a change in the A2ML1 gene that is classified as benign/likely benign — not considered disease-causing, submitted by 4 submitters.

*Reference information, not medical advice, and not a prediction for any individual. A genetic counselor or clinician can interpret what it means for you and your family.*

**Support & next steps:** [Find a genetic counselor (NSGC)](https://findageneticcounselor.nsgc.org/).

## Identity {#identity}

| Field | Value |
| --- | --- |
| Gene | [A2ML1](https://sugi.bio/atlas/gene/A2ML1/) |
| Protein change (HGVS p.) | p.Ser35= |
| Coding change (HGVS c.) | c.105C>T |
| MANE Select transcript | [NM_144670](https://www.ncbi.nlm.nih.gov/nuccore/NM_144670) |
| dbSNP | [rs201185025](https://www.ncbi.nlm.nih.gov/snp/rs201185025/) |
| Variant type | single nucleotide variant |
| Location | chr12:8823224-8823224 (GRCh38) |
| ClinVar | [VCV695806](https://www.ncbi.nlm.nih.gov/clinvar/variation/695806/) |

**All HGVS expressions:** `NC_000012.11:g.8975820C>T`, `NC_000012.12:g.8823224C>T`, `NG_042857.1:g.5753C>T`, `NM_144670.6:c.105C>T`

## Computational & population evidence {#evidence}

**Concordance:** Mixed / partial computational evidence (see below).

- **Missense predictors (AlphaMissense/REVEL/SaProt) do not apply** to this variant type — they score amino-acid substitutions only. For non-missense variants the computational signal comes from conservation and, for splice-region changes, SpliceAI (below), not from a missing predictor score.
- SpliceAI predicts **acceptor loss** (Δ 0.25) — a splice-altering prediction the current classification does not reflect
- Conservation: phyloP -1.132, GERP -3.33 — not a conserved position (phyloP < 0.1, ACGS BP7 cut)
- CADD: **PHRED 8.676**. No single ClinGen-calibrated threshold exists and the expert panels that use CADD disagree — GUCY2D/AIPL1 require ≥ 20.0 for an untranslated-region variant, ABCA4 ≥ 28.1 for a synonymous or indel variant, the Pulmonary Hypertension panel imports Pejaver 2022's missense-calibrated numbers, and the Antibody Deficiencies panel declines CADD entirely for PIK3CD. CADD v1.7 also incorporates Zoonomia phyloP, so it partly re-expresses the conservation above. *Descriptive; no threshold applied.*
- SpliceAI deltas (raw): acceptor loss **0.25**, donor loss **0.01**, acceptor gain **0.15**, donor gain **0.00**. Largest is acceptor loss, 42 bp away.
- SpliceAI deltas (masked): acceptor loss **0.00**, donor loss **0.00**, acceptor gain **0.15**, donor gain **0.00**.
  Masked SpliceAI — what Ensembl VEP and the Broad lookup serve by default — is below the reporting threshold here, so those tools show **no splice signal** for this allele. Masking zeroes a loss scored against a position that is not an annotated splice site, and a gain that merely strengthens an existing one, so the raw score above is describing a cryptic site rather than the site the variant sits on. *No ACMG code is assigned either way.*
- Pangolin: Δ**0.24** (loss), gain 0.10 / loss 0.24. Agrees with SpliceAI. An independent predictor to SpliceAI — a different model trained on different data. *Descriptive; ClinGen's SVI calibration covers SpliceAI, not Pangolin, so no ACMG code is assigned.*
- Population frequency (gnomAD v4.1): grpmax **0.0545%** (nfe) · FAF95 0.051% · FAF99 0.0496% · 643/1,179,992 in the highest group · 697/1,613,848 alleles overall — ultra-rare (popmax 0.0545%, nfe).

| Ancestry group | Allele frequency | 1 in |
| --- | --- | --- |
| European (non-Finnish) (grpmax) | 0.0545% | 1,835 |
| Middle Eastern | 0.0329% | 3,042 |
| Remaining individuals (not grpmax-eligible) | 0.0304% | 3,288 |
| Finnish (not grpmax-eligible) | 0.0187% | 5,335 |
| African / African-American | 0.012% | 8,322 |
| Admixed American | 0.01% | 9,994 |
| South Asian | 0.00549% | 18,206 |
| Ashkenazi Jewish (not grpmax-eligible) | 0.00338% | 29,592 |

*Computational predictors are not independent (ClinGen Variant Classification guidance): AlphaMissense (Cheng et al. 2023) carries the ACMG weight for missense and conservation (phyloP/GERP/phastCons) for non-missense; REVEL (Pejaver-2022 calibrated strength bands) and SaProt (Su et al. 2023, structure-aware, ClinVar-independent protein language model, raw LLR) are shown as orthogonal agreement signals, not additive. For frequency, the gnomAD v4.1 grpmax filtering allele frequency (FAF95) is ClinGen's designated BA1/BS1 input (gnomAD v4 guidance v3.0, June 2025); BA1/BS1 thresholds are disease-specific, not a blanket 5%. Predictions, not a clinical determination.*

## Gene constraint & dosage {#gene-context}

**A2ML1** population constraint: LOEUF 0.953, pLI 1.7127e-40, missense-Z 1.6571. *Lower LOEUF and higher pLI indicate a gene that tolerates loss-of-function poorly; ClinGen dosage is the curated haploinsufficiency call.*

Curated gene–disease validity (ClinGen):

- **Noonan syndrome** — Disputed (AD)

## Protein context {#protein}

Residue **35** lies in a β-strand.

AlphaFold model confidence (whole protein): pLDDT 80.61, 27% of residues very-high.

**5 experimental structure(s)** (PDB): [7Q1Y](https://www.rcsb.org/structure/7Q1Y), [7Q5Z](https://www.rcsb.org/structure/7Q5Z), [7Q60](https://www.rcsb.org/structure/7Q60), [7Q61](https://www.rcsb.org/structure/7Q61), [7Q62](https://www.rcsb.org/structure/7Q62).

## What this gene does {#gene-function}

*Describes the biological roles of A2ML1 (the gene this variant disrupts) — not effects measured for this specific variant. A damaging variant is expected to affect these functions and pathways; the degree depends on the variant.*

**How this variant is thought to act:** A2ML1's established molecular role includes peptidase inhibitor activity.


### Molecular function & processes (GO — experimentally supported) {#go}

**Molecular function:** peptidase inhibitor activity.

**Biological process:** regulation of endopeptidase activity.

## Clinical significance {#significance}

**Benign/Likely benign** — review status Multiple submitters *(criteria provided, multiple submitters, no conflicts)*, last evaluated 2026-01-12.

**Submitter consensus:** conflicting (2 Benign, 2 Likely benign).

**Submission history:** 4 submissions (2019–2026); classifications have differed over time.

### Submitter classifications {#submitters}

| Submitter | Classification | Review | Method | Date |
| --- | --- | --- | --- | --- |
| Women's Health and Genetics/Laboratory Corporation of America, LabCorp | Benign | criteria provided, single submitter | clinical testing | 2021-03-25 |
| GeneDx | Benign | criteria provided, single submitter | clinical testing | 2019-12-26 |
| Labcorp Genetics (formerly Invitae), Labcorp | Likely benign | criteria provided, single submitter | clinical testing | 2026-01-12 |
| Blueprint Genetics | Likely benign | criteria provided, single submitter | clinical testing | 2024-11-15 |

**Reported phenotype names (ClinVar):** not provided, not specified, none provided, AllHighlyPenetrant.

## Similar variants {#similar}

Related A2ML1 variant pages (same residue, condition, or type): [A2ML1 c.1834-1G>T](/variant/a2ml1-c-1834-minus-1g-t), [A2ML1 c.3264+4C>T](/variant/a2ml1-c-3264-plus-4c-t), [A2ML1 c.3933+4A>G](/variant/a2ml1-c-3933-plus-4a-g), [A2ML1 c.409+1G>A](/variant/a2ml1-c-409-plus-1g-a), [A2ML1 c.4221+2T>C](/variant/a2ml1-c-4221-plus-2t-c), [A2ML1 c.*1+1G>A](/variant/a2ml1-c-star-1-plus-1g-a), [A2ML1 p.Ala1002Val](/variant/a2ml1-p-ala1002val), [A2ML1 p.Ala1039Val](/variant/a2ml1-p-ala1039val).

### Data sources & attribution {#sources}

ClinVar (NCBI — public domain, built 2026-10-11); gnomAD v4.1 (Broad Institute, built 2026-10-06); AlphaMissense (Cheng et al. 2023, © Google DeepMind — CC BY 4.0, built 2026-01-27); REVEL (Ioannidis et al. 2016 — ODbL, built 2026-07-13); SaProt (Su et al. 2023 — MIT, built 2026-07-14); SpliceAI (Illumina — free for non-commercial use, built 2026-10-13); CADD (Rentzsch et al. 2019, University of Washington — free for non-commercial use, built 2026-10-10); Conservation (phyloP/phastCons/GERP) (UCSC hg38 470-way mammal (Hiller Lab) + Ensembl Compara, built 2026-07-12); gnomAD Non-coding Constraint (Gnocchi) (Chen et al. 2024, Broad Institute — CC0, built 2026-10-11); gnomAD Regional Missense Constraint (Broad Institute — CC0, built 2026-10-13); Pangolin (Zeng & Li 2022 — CC BY 4.0, built 2026-10-11); Repeat regions (UCSC — RepeatMasker, TRF, segmental duplications, built 2026-10-11); ClinGen (ClinGen, built 2026-09-22); UniProt (CC BY 4.0); Reactome / GO (CC BY 4.0, built 2026-09-23); MaveDB (per-record license, built 2026-10-11); CIViC (CC0, built 2026-09-22); Orphanet (Orphanet, built 2026-06-12)

*Primary record: NCBI ClinVar (variation 695806). Classifications reflect these databases as of the page's build date and may change. Free reference use — not medical advice; consult the primary submitters and a clinician.*