Is IFT88 p.Asp339Val (c.1016A>T) pathogenic?

IFT88 p.Asp339Val (c.1016A>T) is classified Uncertain significance in IFT88 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-11-05). AlphaMissense: likely benign (0.2119); Absent from gnomAD v4.1.

How common is IFT88 p.Asp339Val (c.1016A>T) in the general population?

IFT88 p.Asp339Val (c.1016A>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about IFT88 p.Asp339Val (c.1016A>T)?

AlphaMissense predicts likely benign (score 0.2119) — an in-silico prediction, not a clinical call.

IFT88 p.Asp339Val

c.1016A>T · rs2548164771 · VCV1921272

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.2119 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

1/2 damaging

AlphaMissense, SaProt · REVEL indeterminate

Computational evidence

Protein change
AlphaMissense	0.2119	likely benign
REVEL	0.378	indeterminate
SaProt	LLR -11.43	damaging
⇒ SaProt calls this damaging; AlphaMissense does not; REVEL is indeterminate.
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP 11	GERP 2.2, phastCons 1
Regional constraint	o/e 0.98	unconstrained · MANE · 117 kb · p 0.59 · regional, not allelic
Overall
CADD	26.5	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

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: IFT88
Protein: p.Asp339Val
Coding: c.1016A>T
MANE Select: NM_006531
dbSNP: rs2548164771
Type: single nucleotide variant
Location: chr13:20601908 (GRCh38)
Gene constraint: LOEUF 1.023 · pLI 0.09 (gnomAD)
Structure: AlphaFold pLDDT 77.20

Full IFT88 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

IFT88 p.Ala327Thr Uncertain significance ★★ ⚠ same type
IFT88 p.Ala37Gly Uncertain significance ★★ ⚠ same type
IFT88 p.Ala458Val Uncertain significance ★★ ⚠ same type
IFT88 p.Ala510Pro Uncertain significance ★★ ⚠ same type
IFT88 p.Ala546Thr Uncertain significance ★★ ⚠ same type
IFT88 p.Ala628Ser Uncertain significance ★★ ⚠ same type
IFT88 p.Arg369His Uncertain significance ★★ ⚠ same type
IFT88 p.Arg533Trp 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/ift88-p-asp339val (accessed [today's date]).

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