# NM_144773.4(PROKR2):c.896A>T (p.Asp299Val)

https://sugi.bio/variant/prokr2-p-asp299val

## Summary

**PROKR2 p.Asp299Val (c.896A>T)** is classified **Likely pathogenic** in PROKR2 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-12-17). AlphaMissense: likely pathogenic (0.9673); Very rare (popmax 0.0011%, nfe); Associated with hypogonadotropic hypogonadism 3 with or without anosmia.

**At a glance:** Likely pathogenic · review: Single submitter · 1 submitter · 1 linked condition · AlphaMissense likely pathogenic · very rare (popmax 0.0011%, nfe)

## For patients & families {#patients}

This is a change in the PROKR2 gene that is considered likely disease-causing, submitted by 1 submitter, and is linked to hypogonadotropic hypogonadism 3 with or without anosmia.

*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:** [Condition overview & support (NIH GARD)](https://rarediseases.info.nih.gov/diseases/0003073/index) · [Find a genetic counselor (NSGC)](https://findageneticcounselor.nsgc.org/).

## Identity {#identity}

| Field | Value |
| --- | --- |
| Gene | [PROKR2](https://sugi.bio/atlas/gene/PROKR2/) |
| Protein change (HGVS p.) | p.Asp299Val |
| Coding change (HGVS c.) | c.896A>T |
| MANE Select transcript | [NM_144773](https://www.ncbi.nlm.nih.gov/nuccore/NM_144773) |
| Variant type | single nucleotide variant |
| Location | chr20:5302299-5302299 (GRCh38) |
| ClinVar | [VCV4077446](https://www.ncbi.nlm.nih.gov/clinvar/variation/4077446/) |

**All HGVS expressions:** `NC_000020.10:g.5282945T>A`, `NC_000020.11:g.5302299T>A`, `NG_008132.2:g.17071A>T`, `NM_144773.4:c.896A>T`

## Computational & population evidence {#evidence}

**Concordance:** 1 independent predictor **concordant** with the ClinVar classification.

- AlphaMissense **likely pathogenic** (0.9673) — concordant with the pathogenic call
- REVEL 0.529 (indeterminate)
- SaProt LLR -8.739 (tolerated) — differs from AlphaMissense
- → **In-silico consensus:** AlphaMissense calls this damaging; SaProt does not; REVEL is indeterminate
- Conservation: phyloP 7.869, GERP 1.86, phastCons 1 — highly conserved (agrees)
- AlphaMissense ranks this among the **top 6%** most-pathogenic-predicted substitutions in PROKR2 (of 2,290 modeled).
- CADD: **PHRED 28.8**. 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 0.89** across the covering region of the MANE Select transcript (5,302,043–5,314,369), spanning 12,326 bp. Chi-square p 0.0097. 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 **0.0011%** (nfe) · FAF95 0.000615% · FAF99 0.000474% · 13/1,180,014 in the highest group · 14/1,614,048 alleles overall — very rare (popmax 0.0011%, nfe).

| Ancestry group | Allele frequency | 1 in |
| --- | --- | --- |
| Remaining individuals (not grpmax-eligible) | 0.0016% | 62,508 |
| European (non-Finnish) (grpmax) | 0.0011% | 90,770 |

Remaining individuals shows a higher raw frequency than the grpmax group. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and "Remaining individuals" — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.

*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}

**PROKR2** population constraint: LOEUF 1.492, pLI 4.2632e-10, missense-Z 1.3401. *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):

- **hypogonadotropic hypogonadism 3 with or without anosmia** — Definitive (AD)

## Protein context {#protein}


AlphaFold model confidence (whole protein): pLDDT 78.50, 50% of residues very-high.

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

*Describes the biological roles of PROKR2 (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}

PROKR2 participates in **2 Reactome pathways** (⚕ = disease pathway):

| Pathway (Reactome) | Evidence |
| --- | --- |
| [G alpha (q) signalling events](https://reactome.org/content/detail/R-HSA-416476) | curated |
| [Peptide ligand-binding receptors](https://reactome.org/content/detail/R-HSA-375276) | curated |

## Clinical significance {#significance}

**Likely pathogenic** — review status Single submitter *(criteria provided, single submitter)*, last evaluated 2024-12-17.

**Submitter consensus:** unanimous (1/1 Likely pathogenic).

### Submitter classifications {#submitters}

| Submitter | Classification | Review | Method | Date |
| --- | --- | --- | --- | --- |
| Revvity Omics, Revvity | Likely pathogenic | criteria provided, single submitter | clinical testing | 2024-12-17 |

## Associated conditions {#conditions}

[hypogonadotropic hypogonadism 3 with or without anosmia](https://sugi.bio/atlas/disease/hypogonadotropic-hypogonadism-3-with-or-without-anosmia/).

**Reported phenotype names (ClinVar):** Hypogonadotropic hypogonadism 3 with or without anosmia, PROKR2-Related GnRH Deficiency (Kallmann Syndrome 3), HYPOGONADOTROPIC HYPOGONADISM 3 WITH ANOSMIA.

## Similar variants {#similar}

Related PROKR2 variant pages (same residue, condition, or type): [PROKR2 p.Arg164Gln](/variant/prokr2-p-arg164gln), [PROKR2 p.Glu231Lys](/variant/prokr2-p-glu231lys), [PROKR2 p.Tyr316Ter](/variant/prokr2-p-tyr316ter), [PROKR2 p.Ala103Val](/variant/prokr2-p-ala103val), [PROKR2 p.Ala129Thr](/variant/prokr2-p-ala129thr), [PROKR2 p.Ala156Thr](/variant/prokr2-p-ala156thr), [PROKR2 p.Arg135Cys](/variant/prokr2-p-arg135cys), [PROKR2 p.Arg248Trp](/variant/prokr2-p-arg248trp).

### Data sources & attribution {#sources}

ClinVar (NCBI — public domain, built 2026-10-14); gnomAD v4.1 (Broad Institute, built 2026-10-14); 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 2026-10-14); 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 4077446). 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.*