Is RINT1 p.Ala423Phe (c.1267_1268delinsTT) pathogenic?

RINT1 p.Ala423Phe (c.12671268delinsTT) is classified Uncertain significance in RINT1 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2023-03-23). No gnomAD frequency available for this variant.

How common is RINT1 p.Ala423Phe (c.1267_1268delinsTT) in the general population?

RINT1 p.Ala423Phe (c.1267_1268delinsTT) is no gnomAD frequency available for this variant (gnomAD).

RINT1 p.Ala423Phe

c.1267_1268delinsTT · rs2485133482 · VCV1764354

Uncertain significance Multiple submitters

Classification

Uncertain significance

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 8.2	GERP 3.4, phastCons 1
Regional constraint	o/e 0.96	unconstrained · MANE · 35 kb · p 0.28 · regional, not allelic

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. 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: RINT1
Protein: p.Ala423Phe
Coding: c.1267_1268delinsTT
MANE Select: NM_021930
dbSNP: rs2485133482
Type: Indel
Location: chr7:105550420 (GRCh38)
Gene constraint: LOEUF 0.931 · pLI <0.01 · ClinGen HI 0/3 (gnomAD)
Structure: AlphaFold pLDDT 85.97
Residue 423: the rint1/tip20 domain

Full RINT1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

RINT1 p.Ala423Ser Uncertain significance ★ ⚠ same residue
RINT1 p.Ala423Val Uncertain significance ★ ⚠ same residue
RINT1 c.1334-5_1335delinsTCA Uncertain significance ★★ same type
RINT1 p.Asp594Ile 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/rint1-p-ala423phe (accessed [today's date]).

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