Is CDIPT p.Arg173Trp (c.517C>T) pathogenic?

CDIPT p.Arg173Trp (c.517C>T) is classified Uncertain significance in CDIPT (ClinVar, Single submitter, 1 submitter; last evaluated 2024-03-18). AlphaMissense: likely benign (0.2812); Ultra-rare (popmax 0.067%, mid).

How common is CDIPT p.Arg173Trp (c.517C>T) in the general population?

CDIPT p.Arg173Trp (c.517C>T) is ultra-rare (popmax 0.067%, mid) (gnomAD).

What do computational predictors say about CDIPT p.Arg173Trp (c.517C>T)?

AlphaMissense predicts likely benign (score 0.2812) — an in-silico prediction, not a clinical call.

CDIPT p.Arg173Trp

c.517C>T · rs368954184 · VCV2378423

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.2812 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.067%, mid)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.2812	likely benign
REVEL	0.215	benign-leaning
SaProt	LLR -8.68	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	<0.2	all four deltas below 0.2 · G>T here scores Δ0.25 · evaluated, not missing
Constraint at this position
Conservation	phyloP 10	GERP 0.48, phastCons 1
Regional constraint	o/e 0.89	unconstrained · MANE · 3,665 bp · p 0.068 · regional, not allelic
Overall
CADD	27.9	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 0.067% Middle Eastern · 4/5,968 alleles

Filtering AF 0.0229% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0138%

Overall 0.00453% 71/1,566,592 alleles · ultra-rare

Ancestry group	Frequency	1 in
Middle Easterngrpmax	0.067%	1,492
Admixed American	0.0172%	5,810
South Asian	0.0165%	6,061
Remaining individualsnot grpmax-eligible	0.0148%	6,745
European (non-Finnish)	0.00286%	35,017
East Asian	0.00232%	43,114
African / African-American	0.00135%	74,230

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: CDIPT
Protein: p.Arg173Trp
Coding: c.517C>T
MANE Select: NM_006319
dbSNP: rs368954184
Type: single nucleotide variant
Location: chr16:29859314 (GRCh38)
Gene constraint: LOEUF 1.042 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 90.02

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

Similar variants

CDIPT p.Ala140Ser Uncertain significance ★ ⚠ same type
CDIPT p.Ala146Ser Uncertain significance ★ ⚠ same type
CDIPT p.Ala206Val Uncertain significance ★ ⚠ same type
CDIPT p.Ala22Ser Uncertain significance ★ ⚠ same type
CDIPT p.Ala48Thr Uncertain significance ★ ⚠ same type
CDIPT p.Ala84Val Uncertain significance ★ ⚠ same type
CDIPT p.Arg115Gln Uncertain significance ★ ⚠ same type
CDIPT p.Arg138Lys 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/cdipt-p-arg173trp (accessed [today's date]).

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