Is TTI1 p.Arg477His (c.1430G>A) pathogenic?

TTI1 p.Arg477His (c.1430G>A) is classified Likely benign in TTI1 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-09-14). AlphaMissense: likely benign (0.0904); Ultra-rare (popmax 0.0417%, amr); Associated with Inborn genetic diseases.

What condition is associated with TTI1 p.Arg477His (c.1430G>A)?

TTI1 p.Arg477His (c.1430G>A) is associated with Inborn genetic diseases (ClinVar).

How common is TTI1 p.Arg477His (c.1430G>A) in the general population?

TTI1 p.Arg477His (c.1430G>A) is ultra-rare (popmax 0.0417%, amr) (gnomAD).

What do computational predictors say about TTI1 p.Arg477His (c.1430G>A)?

AlphaMissense predicts likely benign (score 0.0904) — an in-silico prediction, not a clinical call.

TTI1 p.Arg477His

c.1430G>A · rs36038961 · VCV2366341

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0904 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0417%, amr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.0904	likely benign
REVEL	0.184	benign-leaning
SaProt	LLR -8.18	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP 3.3	GERP -0.86, phastCons 1
Regional constraint	o/e 0.91	unconstrained · MANE · 30 kb · p 0.00063 · regional, not allelic
Overall
CADD	18.48	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

Grpmax group 0.0417% Admixed American · 25/60,002 alleles

Filtering AF 0.0289% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0247%

Overall 0.00266% 43/1,614,042 alleles · ultra-rare exomes 39/1,461,880 · genomes 4/152,162 · joint denominator

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.0417%	2,400
East Asian	0.00223%	44,896
Remaining individualsnot grpmax-eligible	0.0016%	62,490
European (non-Finnish)	0.00136%	73,752

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: TTI1
Protein: p.Arg477His
Coding: c.1430G>A
MANE Select: NM_001303457
dbSNP: rs36038961
Type: single nucleotide variant
Location: chr20:38012387 (GRCh38)
Gene constraint: LOEUF 0.78 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 81.38 · 3 PDB
Residue 477: a UniProt-annotated variant site (in nedmim; likely pathogenic)

Full TTI1 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

TTI1 p.Arg477Cys Uncertain significance ★ ⚠ same residue
TTI1 p.Ala806Thr Uncertain significance ★★ ⚠ same condition
TTI1 p.Arg519Gln Uncertain significance ★★ ⚠ same condition
TTI1 p.Arg724Gly Uncertain significance ★★ ⚠ same condition
TTI1 p.Arg869Cys Uncertain significance ★★ same condition
TTI1 p.Cys86Tyr Uncertain significance ★★ ⚠ same condition
TTI1 p.His229Tyr Uncertain significance ★★ ⚠ same condition
TTI1 p.His513Tyr 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/tti1-p-arg477his (accessed [today's date]).

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