Is RTF2 p.Asp168Asn (c.502G>A) pathogenic?

RTF2 p.Asp168Asn (c.502G>A) is classified Uncertain significance in RTF2 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-06-28). AlphaMissense: likely benign (0.2605); No allele count reported in gnomAD v4.1 (AN 1,605,354).

How common is RTF2 p.Asp168Asn (c.502G>A) in the general population?

RTF2 p.Asp168Asn (c.502G>A) is no allele count reported in gnomAD v4.1 (AN 1,605,354) (gnomAD).

What do computational predictors say about RTF2 p.Asp168Asn (c.502G>A)?

AlphaMissense predicts likely benign (score 0.2605) — an in-silico prediction, not a clinical call.

RTF2 p.Asp168Asn

c.502G>A · rs1433826259 · VCV3156836

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.2605 · ACMG-weighted

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,605,354)

Missense predictors

1/2 damaging

AlphaMissense, SaProt · REVEL indeterminate

⚠ Built without this gene's context — gene constraint and dosage, protein structure, pathways, panels and related-variant links were not looked up for this page. why

Computational evidence

Protein change
AlphaMissense	0.2605	likely benign
REVEL	0.329	indeterminate
SaProt	LLR -11.64	damaging
⇒ SaProt calls this damaging; AlphaMissense does not; REVEL is indeterminate.
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP 12	GERP 1.7, phastCons 1
Regional constraint	o/e 0.82	unconstrained · MANE · 50 kb · p 0.00043 · regional, not allelic
Overall
CADD	29.3	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,605,354). 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: RTF2
Protein: p.Asp168Asn
Coding: c.502G>A
MANE Select: NM_016407
dbSNP: rs1433826259
Type: single nucleotide variant
Location: chr20:56513339 (GRCh38)

Full RTF2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

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/rtf2-p-asp168asn (accessed [today's date]).

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