# NM_022124.6(CDH23):c.3070G>A (p.Val1024Met)

https://sugi.bio/variant/cdh23-p-val1024met

## Summary

**CDH23 p.Val1024Met (c.3070G>A)** is classified **Conflicting classifications of pathogenicity** in CDH23 (ClinVar, Conflicting submitters, 5 submitters; last evaluated 2022-09-09). AlphaMissense: likely benign (0.081); Rare (popmax 0.116%, mid).

**At a glance:** Conflicting classifications of pathogenicity · review: Conflicting submitters · rsID rs397517319 · 5 submitters · AlphaMissense likely benign · rare (popmax 0.116%, mid)

## For patients & families {#patients}

This is a change in the CDH23 gene that is of uncertain or conflicting significance (submitters disagree on it), submitted by 5 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 | [CDH23](https://sugi.bio/atlas/gene/CDH23/) |
| Protein change (HGVS p.) | p.Val1024Met |
| Coding change (HGVS c.) | c.3070G>A |
| MANE Select transcript | [NM_022124](https://www.ncbi.nlm.nih.gov/nuccore/NM_022124) |
| dbSNP | [rs397517319](https://www.ncbi.nlm.nih.gov/snp/rs397517319/) |
| Variant type | single nucleotide variant |
| Location | chr10:71707013-71707013 (GRCh38) |
| ClinVar | [VCV45907](https://www.ncbi.nlm.nih.gov/clinvar/variation/45907/) |

**All HGVS expressions:** `NC_000010.10:g.73466770G>A`, `NC_000010.11:g.71707013G>A`, `NG_008835.1:g.315067G>A`, `NM_001171930.2:c.3070G>A`, `NM_001171931.2:c.3070G>A`, `NM_022124.6:c.3070G>A`

## Computational & population evidence {#evidence}

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

- AlphaMissense **likely benign** (0.081)
- REVEL 0.021 (moderately benign-leaning) — agrees with AlphaMissense
- → **In-silico consensus:** AlphaMissense and REVEL both call this tolerated
- Conservation: phyloP 3.862, GERP -0.848, phastCons 1 — highly conserved (differs from AlphaMissense)
- CADD: **PHRED 18.43**. 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 0.96** across the covering region of the MANE Select transcript (71,439,832–71,798,551), spanning 358,719 bp. Chi-square p 0.017. Describes the region, not this allele; gnomAD v4.1.1's own constrained determination. *Descriptive; no ACMG code applied.*
- SpliceAI: **not assessed** — no allele at this position is in our SpliceAI release, either because it lies outside the scored MANE transcript scope or because every allele is below Δ0.2. We cannot tell which, so this claims neither; absence is not evidence against a splicing effect.
- Population frequency (gnomAD v4.1): grpmax **0.116%** (mid) · FAF95 0.0543% · FAF99 0.0384% · 7/6,050 in the highest group · 123/1,607,580 alleles overall — rare (popmax 0.116%, mid).

| Ancestry group | Allele frequency | 1 in |
| --- | --- | --- |
| Middle Eastern (grpmax) | 0.116% | 864 |
| Remaining individuals (not grpmax-eligible) | 0.0177% | 5,659 |
| South Asian | 0.0112% | 8,961 |
| European (non-Finnish) | 0.00714% | 14,014 |
| Admixed American | 0.00676% | 14,792 |
| African / African-American | 0.00667% | 14,994 |
| Ashkenazi Jewish (not grpmax-eligible) | 0.00339% | 29,464 |
| East Asian | 0.00224% | 44,622 |

*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}

**CDH23** population constraint: LOEUF 0.685, pLI 2.8869e-32, missense-Z 1.6119; ClinGen dosage — haploinsufficiency 30, triplosensitivity Not yet evaluated (0–3 scale). *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** — Definitive (AR)

## Protein context {#protein}

Residue **1024** lies in the cadherin 10 domain.

**6 experimental structure(s)** (PDB): [2KBR](https://www.rcsb.org/structure/2KBR), [2KBS](https://www.rcsb.org/structure/2KBS), [2LSR](https://www.rcsb.org/structure/2LSR), [5TFM](https://www.rcsb.org/structure/5TFM), [5VVM](https://www.rcsb.org/structure/5VVM), [5WJ8](https://www.rcsb.org/structure/5WJ8).

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

*Describes the biological roles of CDH23 (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.*


### Pathways affected {#pathways}

CDH23 participates in **2 Reactome pathways** (⚕ = disease pathway):

| Pathway (Reactome) | Evidence |
| --- | --- |
| [Sensory processing of sound by inner hair cells of the cochlea](https://reactome.org/content/detail/R-HSA-9662360) | electronic |
| [Sensory processing of sound by outer hair cells of the cochlea](https://reactome.org/content/detail/R-HSA-9662361) | electronic |

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

**Biological process:** calcium ion transport, sensory perception of sound, photoreceptor cell maintenance, sensory perception of light stimulus, equilibrioception, regulation of cytosolic calcium ion concentration.

## Clinical significance {#significance}

**Conflicting classifications of pathogenicity** — review status Conflicting submitters *(criteria provided, conflicting classifications)*, last evaluated 2022-09-09.

**Submitter consensus:** conflicting (4 Uncertain significance, 1 Likely benign).

**Submission history:** 5 submissions (2014–2024); classifications have differed over time.

### Submitter classifications {#submitters}

| Submitter | Classification | Review | Method | Date |
| --- | --- | --- | --- | --- |
| Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Likely benign | criteria provided, single submitter | clinical testing | 2014-08-11 |
| CeGaT Center for Human Genetics Tuebingen | Uncertain significance | criteria provided, single submitter | clinical testing | 2019-01-01 |
| Labcorp Genetics (formerly Invitae), Labcorp | Uncertain significance | criteria provided, single submitter | clinical testing | 2022-08-20 |
| GeneDx | Uncertain significance | criteria provided, single submitter | clinical testing | 2022-09-09 |
| PreventionGenetics, part of Exact Sciences | Uncertain significance | no assertion criteria provided | clinical testing | 2024-09-12 |

**Reported phenotype names (ClinVar):** not specified, not provided, CDH23-related disorder, CDH23-related condition, CDH23-related disorders, AllHighlyPenetrant, none provided.

## Similar variants {#similar}

Related CDH23 variant pages (same residue, condition, or type): [CDH23 p.Val1024=](/variant/cdh23-p-val1024), [CDH23 p.Arg2029Trp](/variant/cdh23-p-arg2029trp), [CDH23 p.Asp127Gly](/variant/cdh23-p-asp127gly), [CDH23 p.Glu956Lys](/variant/cdh23-p-glu956lys), [CDH23 p.Pro240Leu](/variant/cdh23-p-pro240leu), [CDH23 c.1515-12G>A](/variant/cdh23-c-1515-minus-12g-a), [CDH23 p.Ala3190Val](/variant/cdh23-p-ala3190val), [CDH23 p.Arg301Gln](/variant/cdh23-p-arg301gln).

### 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 45907). 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.*