Is TTI2 p.Asp54Tyr (c.160G>T) pathogenic?

TTI2 p.Asp54Tyr (c.160G>T) is classified Uncertain significance in TTI2 (ClinVar, Single submitter, 1 submitter; last evaluated 2019-05-21). AlphaMissense: likely benign (0.1335); Ultra-rare (popmax 0.0527%, sas); Associated with severe intellectual disability-short stature-behavioral abnormalities-facial dysmorphism syndrome.

How common is TTI2 p.Asp54Tyr (c.160G>T) in the general population?

TTI2 p.Asp54Tyr (c.160G>T) is ultra-rare (popmax 0.0527%, sas) (gnomAD).

What do computational predictors say about TTI2 p.Asp54Tyr (c.160G>T)?

AlphaMissense predicts likely benign (score 0.1335) — an in-silico prediction, not a clinical call.

TTI2 p.Asp54Tyr

Q: What condition is associated with TTI2 p.Asp54Tyr (c.160G>T)?

TTI2 p.Asp54Tyr (c.160G>T) is associated with severe intellectual disability-short stature-behavioral abnormalities-facial dysmorphism syndrome (ClinVar).

c.160G>T · rs577201836 · VCV2437396

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1335 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0527%, sas)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

severe intellectual disability-short stature-behavioral abnormalities-facial dysmorphism syndrome

Computational evidence

Protein change
AlphaMissense	0.1335	likely benign
REVEL	0.283	benign-leaning
SaProt	LLR -7.06	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 3.8	GERP 2.1, phastCons 1
Regional constraint	o/e 0.95	unconstrained · MANE · 13 kb · p 0.23 · regional, not allelic
Overall
CADD	23.6	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 0.0527% South Asian · 48/91,086 alleles

Filtering AF 0.0408% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0366%

Overall 0.00316% 51/1,614,118 alleles · ultra-rare exomes 47/1,461,802 · genomes 4/152,316 · joint denominator

Ancestry group	Frequency	1 in
South Asiangrpmax	0.0527%	1,898
Remaining individualsnot grpmax-eligible	0.0032%	31,253
East Asian	0.00223%	44,876

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: TTI2
Protein: p.Asp54Tyr
Coding: c.160G>T
MANE Select: NM_001102401
dbSNP: rs577201836
Type: single nucleotide variant
Location: chr8:33512454 (GRCh38)
Gene constraint: LOEUF 0.758 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 84.85 · 2 PDB

Full TTI2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

severe intellectual disability-short stature-behavioral abnormalities-facial dysmorphism syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

TTI2 p.Arg334Gln Uncertain significance ★★ ⚠ same condition
TTI2 p.Arg355His Uncertain significance ★★ ⚠ same condition
TTI2 p.Thr232Ile Uncertain significance ★★ ⚠ same condition
TTI2 c.-99-31C>T Benign ★★ same condition
TTI2 p.Asn46= Benign ★★ same condition
TTI2 p.Glu63Gly Benign ★★ same condition
TTI2 c.1115+1G>A Likely pathogenic ★ same condition
TTI2 c.1115+2T>C Likely pathogenic ★ 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/tti2-p-asp54tyr (accessed [today's date]).

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