# NM_001135022.2(ELMOD3):c.178G>T (p.Ala60Ser)

https://sugi.bio/variant/elmod3-p-ala60ser

## Summary

**ELMOD3 p.Ala60Ser (c.178G>T)** is classified **Uncertain significance** in ELMOD3 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-03-06). AlphaMissense: likely benign (0.0818); Absent from gnomAD v4.1.

**At a glance:** Uncertain significance · review: Single submitter · 1 submitter · AlphaMissense likely benign · absent from gnomAD v4.1

## For patients & families {#patients}

This is a change in the ELMOD3 gene that is currently of uncertain significance — a definitive interpretation has not yet been established, submitted by 1 submitter.

*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 | [ELMOD3](https://sugi.bio/atlas/gene/ELMOD3/) |
| Protein change (HGVS p.) | p.Ala60Ser |
| Coding change (HGVS c.) | c.178G>T |
| MANE Select transcript | [NM_001135022](https://www.ncbi.nlm.nih.gov/nuccore/NM_001135022) |
| Variant type | single nucleotide variant |
| Location | chr2:85363145-85363145 (GRCh38) |
| ClinVar | [VCV3844491](https://www.ncbi.nlm.nih.gov/clinvar/variation/3844491/) |

**All HGVS expressions:** `NC_000002.11:g.85590268G>T`, `NC_000002.12:g.85363145G>T`, `NG_051291.1:g.13752G>T`, `NM_001135021.2:c.178G>T`, `NM_001135022.2:c.178G>T`, `NM_001135023.2:c.178G>T`, `NM_001329791.2:c.178G>T`, `NM_001329792.2:c.178G>T`, `NM_001329793.2:c.178G>T`, `NM_032213.5:c.178G>T`, `NR_138131.2:n.566G>T`, `NR_138132.2:n.908G>T`, `NR_138133.2:n.471G>T`

## Computational & population evidence {#evidence}

**Concordance:** ClinVar classifies this **uncertain**; the computational predictors unanimously lean **tolerated** — a triage signal, not a reclassification.

- AlphaMissense **likely benign** (0.0818)
- REVEL 0.031 (moderately benign-leaning) — agrees with AlphaMissense
- SaProt LLR -5.548 (tolerated) — agrees with AlphaMissense
- → **In-silico consensus:** AlphaMissense, REVEL and SaProt all call this tolerated
- SpliceAI predicts **acceptor loss** (Δ 0.24) — a splice-altering prediction on an uncertain variant — a signal for review
- Conservation: phyloP 1.084, GERP -0.504, phastCons 0.01 — weakly conserved position
- CADD: **PHRED 12.61**. 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.*
- Regional missense constraint: **o/e 0.87** across the covering region of the MANE Select transcript (85,357,199–85,390,959), spanning 33,760 bp. Chi-square p 0.0055. Describes the region, not this allele; gnomAD v4.1.1's own constrained determination. *Descriptive; no ACMG code applied.*
- SpliceAI deltas (raw): acceptor loss **0.24**, donor loss **0.22**, acceptor gain **0.00**, donor gain **0.00**. Largest is acceptor loss.
- SpliceAI deltas (masked): acceptor loss **0.00**, donor loss **0.22**, acceptor gain **0.00**, donor gain **0.00**.
- Pangolin: Δ**0.22** (loss), gain 0.00 / loss 0.22. 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: **absent from gnomAD v4.1** — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

*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}

**ELMOD3** population constraint: LOEUF 1.021, pLI 2.1153e-08, missense-Z 1.1518. *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):

- **nonsyndromic genetic hearing loss** — Limited (AD)
- **nonsyndromic genetic hearing loss** — Limited (AR)

## Protein context {#protein}


AlphaFold model confidence (whole protein): pLDDT 76.18, 54% of residues very-high.

## Clinical significance {#significance}

**Uncertain significance** — review status Single submitter *(criteria provided, single submitter)*, last evaluated 2025-03-06.

**Submitter consensus:** unanimous (1/1 Uncertain significance).

### Submitter classifications {#submitters}

| Submitter | Classification | Review | Method | Date |
| --- | --- | --- | --- | --- |
| Ambry Genetics | Uncertain significance | criteria provided, single submitter | clinical testing | 2025-03-06 |

**Reported phenotype names (ClinVar):** not specified, AllHighlyPenetrant.

## Similar variants {#similar}

Related ELMOD3 variant pages (same residue, condition, or type): [ELMOD3 p.Ala234Val](/variant/elmod3-p-ala234val), [ELMOD3 p.Ala289Val](/variant/elmod3-p-ala289val), [ELMOD3 p.Ala38Thr](/variant/elmod3-p-ala38thr), [ELMOD3 p.Gln100Ter](/variant/elmod3-p-gln100ter), [ELMOD3 p.Gln371Ter](/variant/elmod3-p-gln371ter), [ELMOD3 p.His294Tyr](/variant/elmod3-p-his294tyr), [ELMOD3 p.His297Tyr](/variant/elmod3-p-his297tyr), [ELMOD3 p.Leu164Met](/variant/elmod3-p-leu164met).

### 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 3844491). 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.*