Is IFT27 p.Val16Ala (c.47T>C) pathogenic?

IFT27 p.Val16Ala (c.47T>C) is classified Uncertain significance in IFT27 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-06-12). AlphaMissense: likely benign (0.2641); Absent from gnomAD v4.1.

How common is IFT27 p.Val16Ala (c.47T>C) in the general population?

IFT27 p.Val16Ala (c.47T>C) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about IFT27 p.Val16Ala (c.47T>C)?

AlphaMissense predicts likely benign (score 0.2641) — an in-silico prediction, not a clinical call.

IFT27 p.Val16Ala

c.47T>C · rs1938294510 · VCV1716552

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.2641 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

1/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.2641	likely benign
REVEL	0.867	moderately pathogenic-leaning
SaProt	LLR -8.49	tolerated
⇒ REVEL calls this damaging; AlphaMissense and SaProt do not.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 9.2	GERP 1.2, phastCons 1
Regional constraint	o/e 0.90	unconstrained · MANE · 17 kb · p 0.13 · regional, not allelic
Overall
CADD	25.0	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: IFT27
Protein: p.Val16Ala
Coding: c.47T>C
MANE Select: NM_001177701
dbSNP: rs1938294510
Type: single nucleotide variant
Location: chr22:36767850 (GRCh38)
Gene constraint: LOEUF 1.078 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 92.65
Residue 16: a binding site

Full IFT27 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

IFT27 p.Tyr36Cys Pathogenic ★★ same type
IFT27 c.114+5G>T Uncertain significance ★★ same type
IFT27 p.Arg26Cys Uncertain significance ★★ ⚠ same type
IFT27 p.Arg26His Uncertain significance ★★ ⚠ same type
IFT27 p.Leu44Phe Uncertain significance ★★ same type
IFT27 p.Lys3Gln Uncertain significance ★★ ⚠ same type
IFT27 c.114+8G>A Likely benign ★★ same type
IFT27 c.174+17C>T Likely benign ★★ 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/ift27-p-val16ala (accessed [today's date]).

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