# NM_001379228.1(MRAP):c.486C>G (p.Pro162=)

https://sugi.bio/variant/mrap-p-pro162

## Summary

**MRAP p.Pro162= (c.486C>G)** is classified **Uncertain significance** in MRAP (ClinVar, Single submitter, 1 submitter; last evaluated 2018-01-12). Ultra-rare (popmax 0.0164%, mid); Associated with glucocorticoid deficiency 2.

**At a glance:** Uncertain significance · review: Single submitter · rsID rs146788457 · 1 submitter · 1 linked condition · ultra-rare (popmax 0.0164%, mid)

## For patients & families {#patients}

This is a change in the MRAP gene that is currently of uncertain significance — a definitive interpretation has not yet been established, submitted by 1 submitter, and is linked to glucocorticoid deficiency 2.

*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.*

|  |  |
| --- | --- |
| Typical inheritance (of this condition) | Autosomal recessive |
| Age of onset (of this condition) | Childhood, Infancy |
| Prevalence | 1-9 / 1 000 000 (Ireland) |
| Diagnostic panels | MRAP is a diagnostic-grade gene on 1 Genomics England panel |

**Commonly reported features of Familial glucocorticoid deficiency** (across patients with this condition; presentation varies — frequencies from Orphanet):

- Adrenal insufficiency — Obligate (100%)
- Decreased circulating cortisol level — Obligate (100%)
- Failure to thrive — Very frequent (99-80%)
- Hypotension — Very frequent (99-80%)
- Generalized hyperpigmentation — Very frequent (99-80%)
- Abnormality of circulating adrenocorticotropin level — Very frequent (99-80%)
- Ketotic hypoglycemia — Very frequent (99-80%)
- Impaired cortisol response to insulin stimulation test — Very frequent (99-80%)

**Support & next steps:** [Condition overview & support (NIH GARD)](https://rarediseases.info.nih.gov/diseases/0015412/index) · [Find a genetic counselor (NSGC)](https://findageneticcounselor.nsgc.org/).

## Identity {#identity}

| Field | Value |
| --- | --- |
| Gene | [MRAP](https://sugi.bio/atlas/gene/MRAP/) |
| Protein change (HGVS p.) | p.Pro162= |
| Coding change (HGVS c.) | c.486C>G |
| MANE Select transcript | [NM_001379228](https://www.ncbi.nlm.nih.gov/nuccore/NM_001379228) |
| dbSNP | [rs146788457](https://www.ncbi.nlm.nih.gov/snp/rs146788457/) |
| Variant type | single nucleotide variant |
| Location | chr21:32311963-32311963 (GRCh38) |
| ClinVar | [VCV339685](https://www.ncbi.nlm.nih.gov/clinvar/variation/339685/) |

**All HGVS expressions:** `NC_000021.8:g.33684274C>G`, `NC_000021.9:g.32311963C>G`, `NG_016234.1:g.25151C>G`, `NM_001285394.2:c.309C>G`, `NM_001379228.1:c.486C>G`, `NM_014825.3:c.*2955G>C`, `NM_178817.4:c.486C>G`, `NM_206898.2:c.207-2588C>G`

## 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 (below), not from a missing predictor score.
- Conservation: phyloP -0.19, GERP 0.139 — not a conserved position (phyloP < 0.1, ACGS BP7 cut)
- CADD: **PHRED 2.429**. 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: **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 **0.0164%** (mid) · FAF95 0.00426% · FAF99 0.00387% · 1/6,084 in the highest group · 212/1,613,366 alleles overall — ultra-rare (popmax 0.0164%, mid).

| Ancestry group | Allele frequency | 1 in |
| --- | --- | --- |
| Ashkenazi Jewish (not grpmax-eligible) | 0.422% | 237 |
| Remaining individuals (not grpmax-eligible) | 0.0288% | 3,471 |
| Middle Eastern (grpmax) | 0.0164% | 6,084 |
| Admixed American | 0.00833% | 12,002 |
| European (non-Finnish) | 0.00534% | 18,731 |

Ashkenazi Jewish 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}

**MRAP** population constraint: LOEUF 1.44, pLI 0.0032169, missense-Z -0.18356. *Lower LOEUF and higher pLI indicate a gene that tolerates loss-of-function poorly; ClinGen dosage is the curated haploinsufficiency call.*

## Protein context {#protein}

Residue **162** lies in the 'disordered' region.

AlphaFold model confidence (whole protein): pLDDT 58.50, 11% of residues very-high.

**1 experimental structure(s)** (PDB): [8GY7](https://www.rcsb.org/structure/8GY7).

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

*Describes the biological roles of MRAP (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:** MRAP's established molecular role includes corticotropin hormone receptor binding. p.Pro162= falls in the disordered region.


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

**Molecular function:** corticotropin hormone receptor binding, type 3 melanocortin receptor binding, type 4 melanocortin receptor binding, type 5 melanocortin receptor binding, identical protein binding, type 1 melanocortin receptor binding.

**Biological process:** protein localization to plasma membrane, positive regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway, negative regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway, negative regulation of protein localization to plasma membrane.

## Clinical significance {#significance}

**Uncertain significance** — review status Single submitter *(criteria provided, single submitter)*, last evaluated 2018-01-12.

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

### Submitter classifications {#submitters}

| Submitter | Classification | Review | Method | Date |
| --- | --- | --- | --- | --- |
| Illumina Laboratory Services, Illumina | Uncertain significance | criteria provided, single submitter | clinical testing | 2018-01-12 |

## Associated conditions {#conditions}

[glucocorticoid deficiency 2](https://sugi.bio/atlas/disease/glucocorticoid-deficiency-2/).

**Reported phenotype names (ClinVar):** Glucocorticoid deficiency 2, FAMILIAL GLUCOCORTICOID DEFICIENCY 2.

## Similar variants {#similar}

Related MRAP variant pages (same residue, condition, or type): [MRAP p.Pro162Thr](/variant/mrap-p-pro162thr), [MRAP c.106+1G>C](/variant/mrap-c-106-plus-1g-c), [MRAP p.Met1Ile](/variant/mrap-p-met1ile), [MRAP c.*108A>G](/variant/mrap-c-star-108a-g), [MRAP p.Thr130Ile](/variant/mrap-p-thr130ile), [MRAP c.106+1G>A](/variant/mrap-c-106-plus-1g-a), [MRAP c.106+15G>C](/variant/mrap-c-106-plus-15g-c), [MRAP c.-151+125C>T](/variant/mrap-c-minus-151-plus-125c-t).

### 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 339685). 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.*