Is IFT27 p.Ala128= (c.384C>T) pathogenic?

IFT27 p.Ala128= (c.384C>T) is classified Likely benign in IFT27 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-12-05). Very rare (popmax 0.00449%, sas).

How common is IFT27 p.Ala128= (c.384C>T) in the general population?

IFT27 p.Ala128= (c.384C>T) is very rare (popmax 0.00449%, sas) (gnomAD).

IFT27 p.Ala128=

c.384C>T · rs755859739 · VCV782352

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00449%, sas)

⚠ Built without this gene's context — gene constraint and dosage, protein structure, pathways, panels and related-variant links were not looked up for this page. why

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP 0.1	GERP -1.8
Overall
CADD	7.841	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00449% South Asian · 4/89,154 alleles

Filtering AF 0.00216% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00191%

Overall 0.00262% 42/1,605,758 alleles · very rare exomes 40/1,453,538 · genomes 2/152,220 · joint denominator

Ancestry group	Frequency	1 in
South Asiangrpmax	0.00449%	22,288
European (non-Finnish)	0.00298%	33,581
Admixed American	0.00168%	59,362
Remaining individualsnot grpmax-eligible	0.00161%	62,150
African / African-American	0.00134%	74,782

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: IFT27
Protein: p.Ala128=
Coding: c.384C>T
MANE Select: NM_001177701
dbSNP: rs755859739
Type: single nucleotide variant
Location: chr22:36762982 (GRCh38)

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

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-ala128 (accessed [today's date]).

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