Is TPRN p.Pro161= (c.483G>A) pathogenic?

TPRN p.Pro161= (c.483G>A) is classified Likely benign in TPRN (ClinVar, Single submitter, 1 submitter; last evaluated 2019-01-17). No allele count reported in gnomAD v4.1 (AN 960,530).

How common is TPRN p.Pro161= (c.483G>A) in the general population?

TPRN p.Pro161= (c.483G>A) is no allele count reported in gnomAD v4.1 (AN 960,530) (gnomAD).

TPRN p.Pro161=

c.483G>A · rs1834784292 · VCV1202908

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 960,530)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP -1.3	GERP -1.6
Overall
CADD	7.272	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 960,530). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: TPRN
Protein: p.Pro161=
Coding: c.483G>A
MANE Select: NM_001128228
dbSNP: rs1834784292
Type: single nucleotide variant
Location: chr9:137200229 (GRCh38)
Gene constraint: LOEUF 1.099 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 55.27 · 1 PDB
Residue 161: the 'disordered' region

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

Similar variants

TPRN p.Pro161Leu Uncertain significance ★ ⚠ same residue
TPRN p.Gln414Ter Pathogenic ★★ same type
TPRN c.1725+5G>A Uncertain significance ★★ same type
TPRN p.Ala191Val Uncertain significance ★★ ⚠ same type
TPRN p.Ala302Asp Uncertain significance ★★ ⚠ same type
TPRN p.Ala390Ser Uncertain significance ★★ ⚠ same type
TPRN p.Ala695Thr Uncertain significance ★★ ⚠ same type
TPRN p.Arg231Trp 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/tprn-p-pro161 (accessed [today's date]).

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