Is IGF1 c.*784A>C pathogenic?

IGF1 c.784A>C is classified Likely benign in IGF1 (ClinVar, Single submitter, 1 submitter; last evaluated 2018-01-13). Rare (popmax 0.311%, sas); Associated with growth delay due to insulin-like growth factor type 1 deficiency.

What condition is associated with IGF1 c.*784A>C?

IGF1 c.*784A>C is associated with growth delay due to insulin-like growth factor type 1 deficiency (ClinVar).

How common is IGF1 c.*784A>C in the general population?

IGF1 c.*784A>C is rare (popmax 0.311%, sas) (gnomAD).

IGF1 c.*784A>C

Q: How is Growth delay due to insulin-like growth factor type 1 deficiency inherited?

Typically Autosomal recessive (Orphanet). A genetic counselor can assess individual risk for a family.

rs5742701 · VCV881948

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

rare (popmax 0.311%, sas)

Conditions

growth delay due to insulin-like growth factor type 1 deficiency

⚠ 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 0.29	GERP -2, phastCons 1
Non-coding constraint	Z -0.94	1 kb window · o/e 1.07 · regional · uncalibrated
Overall
CADD	1.484	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.311% South Asian · 15/4,822 alleles

Filtering AF 0.192% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.155%

Overall 0.0105% 16/152,780 alleles · rare exomes 0/436 · genomes 16/152,344 · joint denominator

Ancestry group	Frequency	1 in
South Asiangrpmax	0.311%	321
Remaining individualsnot grpmax-eligible	0.0472%	2,120

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: IGF1
Coding: c.*784A>C
MANE Select: NM_000618
dbSNP: rs5742701
Type: single nucleotide variant
Location: chr12:102401723 (GRCh38)

Full IGF1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

growth delay due to insulin-like growth factor type 1 deficiency — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Growth delay due to insulin-like growth factor type 1 deficiency (Orphanet):

Inheritance: Autosomal recessive
Onset: Antenatal, Infancy, Neonatal

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/igf1-c-star-784a-c (accessed [today's date]).

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