Is RPS19 p.Pro47= (c.141C>T) pathogenic?

RPS19 p.Pro47= (c.141C>T) is classified Likely benign in RPS19 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-08-09). Very rare (popmax 0.00167%, amr); Associated with Diamond-Blackfan anemia.

What condition is associated with RPS19 p.Pro47= (c.141C>T)?

RPS19 p.Pro47= (c.141C>T) is associated with Diamond-Blackfan anemia (ClinVar).

How common is RPS19 p.Pro47= (c.141C>T) in the general population?

RPS19 p.Pro47= (c.141C>T) is very rare (popmax 0.00167%, amr) (gnomAD).

How is Diamond-Blackfan anemia inherited?

Typically Autosomal dominant (Orphanet). A genetic counselor can assess individual risk for a family.

RPS19 p.Pro47=

c.141C>T · rs143577980 · VCV2148219

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00167%, amr)

Conditions

Diamond-Blackfan anemia

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 0.28	GERP 0.7, phastCons 0.98
Overall
CADD	13.65	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00167% Admixed American · 1/60,002 alleles

Overall 0.000124% 2/1,613,926 alleles · very rare

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.00167%	60,002
European (non-Finnish)	8.47e-05%	1,179,976

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: RPS19
Protein: p.Pro47=
Coding: c.141C>T
MANE Select: NM_001022
dbSNP: rs143577980
Type: single nucleotide variant
Location: chr19:41861181 (GRCh38)
Gene constraint: LOEUF 0.239 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 92.01 · 205 PDB
Residue 47: a UniProt-annotated variant site (in dba1; affects assembly into a functional ribosomal subunit)

Full RPS19 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Diamond-Blackfan anemia — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Diamond-Blackfan anemia (Orphanet):

Inheritance: Autosomal dominant
Onset: Childhood, Infancy, Neonatal
Prevalence: 1-9 / 1 000 000 (Europe)

Similar variants

RPS19 p.Pro47Leu Likely pathogenic ★ same residue
RPS19 p.Pro47Ser Uncertain significance ★ ⚠ same residue
RPS19 c.356+1G>A Likely pathogenic ★★ same condition
RPS19 c.412-2A>G Pathogenic/Likely pathogenic ★★ same condition
RPS19 p.Arg56Leu Likely pathogenic ★★ same condition
RPS19 p.Arg62Gln Pathogenic ★★ same condition
RPS19 p.Arg62Trp Pathogenic/Likely pathogenic ★★ same condition
RPS19 p.Arg94Ter Pathogenic ★★ same condition

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/rps19-p-pro47 (accessed [today's date]).

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