Is RIN2 p.Arg73Trp (c.217C>T) pathogenic?

RIN2 p.Arg73Trp (c.217C>T) is classified Uncertain significance in RIN2 (ClinVar, Multiple submitters, 5 submitters; last evaluated 2024-02-28). AlphaMissense: likely benign (0.2343); Ultra-rare (popmax 0.0822%, mid); Associated with Inborn genetic diseases.

What condition is associated with RIN2 p.Arg73Trp (c.217C>T)?

RIN2 p.Arg73Trp (c.217C>T) is associated with Inborn genetic diseases (ClinVar).

How common is RIN2 p.Arg73Trp (c.217C>T) in the general population?

RIN2 p.Arg73Trp (c.217C>T) is ultra-rare (popmax 0.0822%, mid) (gnomAD).

What do computational predictors say about RIN2 p.Arg73Trp (c.217C>T)?

AlphaMissense predicts likely benign (score 0.2343) — an in-silico prediction, not a clinical call.

RIN2 p.Arg73Trp

c.217C>T · rs372531454 · VCV624190

Uncertain significance Multiple submitters

Classification

Uncertain significance

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 5 submitters

AlphaMissense

likely benign

0.2343 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0822%, mid)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.2343	likely benign
REVEL	0.137	moderately benign-leaning
SaProt	LLR -8.58	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 2.3	GERP -1.7, phastCons 0.98
Regional constraint	o/e 1.06	unconstrained · MANE · 86 kb · p 0.14 · regional, not allelic
Overall
CADD	26.3	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

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

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0822% Middle Eastern · 5/6,084 alleles

Filtering AF 0.0323% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.021%

Overall 0.0148% 238/1,612,932 alleles · ultra-rare exomes 224/1,460,844 · genomes 14/152,088 · joint denominator

Ancestry group	Frequency	1 in
Middle Easterngrpmax	0.0822%	1,217
Remaining individualsnot grpmax-eligible	0.024%	4,162
South Asian	0.022%	4,542
European (non-Finnish)	0.0161%	6,209
Admixed American	0.01%	9,980
Finnishnot grpmax-eligible	0.00313%	31,963

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: RIN2
Protein: p.Arg73Trp
Coding: c.217C>T
MANE Select: NM_018993
dbSNP: rs372531454
Type: single nucleotide variant
Location: chr20:19956673 (GRCh38)
Gene constraint: LOEUF 0.637 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 64.30

Full RIN2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

RIN2 p.Arg73Gln Uncertain significance ★★ ⚠ same residue
RIN2 p.Ala205Val Uncertain significance ★★ ⚠ same condition
RIN2 p.Ala72Thr Uncertain significance ★★ ⚠ same condition
RIN2 p.Arg135Cys Uncertain significance ★★ ⚠ same condition
RIN2 p.Arg170Trp Uncertain significance ★★ ⚠ same condition
RIN2 p.Arg255Thr Uncertain significance ★★ ⚠ same condition
RIN2 p.Arg290Leu Uncertain significance ★★ ⚠ same condition
RIN2 p.Arg303Gln Uncertain significance ★★ ⚠ 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/rin2-p-arg73trp (accessed [today's date]).

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