Is MRAP p.Pro95= (c.285G>A) pathogenic?

MRAP p.Pro95= (c.285G>A) is classified Likely benign in MRAP (ClinVar, Single submitter, 1 submitter; last evaluated 2023-01-01). Very rare (popmax 0.00668%, eas).

How common is MRAP p.Pro95= (c.285G>A) in the general population?

MRAP p.Pro95= (c.285G>A) is very rare (popmax 0.00668%, eas) (gnomAD).

MRAP p.Pro95=

c.285G>A · rs779122471 · VCV2652592

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00668%, eas)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -0.46	GERP -2.4
Overall
CADD	1.574	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00668% East Asian · 3/44,890 alleles

Filtering AF 0.00177% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000891%

Overall 0.00173% 28/1,614,012 alleles · very rare exomes 26/1,461,806 · genomes 2/152,206 · joint denominator

Ancestry group	Frequency	1 in
East Asiangrpmax	0.00668%	14,963
South Asian	0.00329%	30,360
Remaining individualsnot grpmax-eligible	0.0032%	31,241
Admixed American	0.00167%	60,008
European (non-Finnish)	0.00153%	65,557
African / African-American	0.00133%	74,926

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: MRAP
Protein: p.Pro95=
Coding: c.285G>A
MANE Select: NM_001379228
dbSNP: rs779122471
Type: single nucleotide variant
Location: chr21:32311762 (GRCh38)
Gene constraint: LOEUF 1.44 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 58.50 · 1 PDB

Full MRAP gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

MRAP c.106+1G>C Pathogenic ★★ same type
MRAP p.Met1Ile Pathogenic ★★ same type
MRAP c.*108A>G Benign ★★ same type
MRAP p.Thr130Ile Benign ★★ same type
MRAP c.106+1G>A Pathogenic ★ same type
MRAP p.Met1Val Pathogenic ★ same type
MRAP c.106+15G>C Uncertain significance ★ same type
MRAP c.-151+125C>T Uncertain significance ★ same type

Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →

Cite Sugi Variant

Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/mrap-p-pro95 (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown