Is GHSR p.Arg159= (c.477G>A) pathogenic?

GHSR p.Arg159= (c.477G>A) is classified Benign in GHSR (ClinVar, Multiple submitters, 7 submitters; last evaluated 2026-05-08). Common (popmax 43.3%, eas) — too common for a highly-penetrant pathogenic allele; Associated with short stature due to GHSR deficiency.

What condition is associated with GHSR p.Arg159= (c.477G>A)?

GHSR p.Arg159= (c.477G>A) is associated with short stature due to GHSR deficiency (ClinVar).

How is Short stature due to GHSR deficiency inherited?

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

GHSR p.Arg159=

Q: How common is GHSR p.Arg159= (c.477G>A) in the general population?

GHSR p.Arg159= (c.477G>A) is common (popmax 43.3%, eas) — too common for a highly-penetrant pathogenic allele (gnomAD).

c.477G>A · rs572169 · VCV263110

Benign Multiple submitters

Classification

Benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 7 submitters

gnomAD v4.1

Common

common (popmax 43.3%, eas) — too common for a highly-penetrant pathogenic allele

Conditions

short stature due to GHSR deficiency

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -1.6	GERP -3.9
Overall
CADD	5.513	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 43.3% East Asian · 19,377/44,798 alleles

Filtering AF 42.7% ClinGen BA1/BS1 input FAF95, joint · FAF99 42.5%

Overall 29.9% 482,598/1,612,494 alleles · common

Ancestry group	Frequency	1 in
East Asiangrpmax	43.3%	2
Amishnot grpmax-eligible	38.9%	3
Admixed American	38.1%	3
Finnishnot grpmax-eligible	33.4%	3
European (non-Finnish)	31.2%	3
Remaining individualsnot grpmax-eligible	28.2%	4
South Asian	22.9%	4
Ashkenazi Jewishnot grpmax-eligible	19.4%	5
Middle Eastern	17.2%	6
African / African-American	7.9%	13

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: GHSR
Protein: p.Arg159=
Coding: c.477G>A
MANE Select: NM_198407
dbSNP: rs572169
Type: single nucleotide variant
Location: chr3:172447937 (GRCh38)
Gene constraint: LOEUF 1.033 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 81.75 · 10 PDB
Residue 159: a disulfide bond; an α-helix

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

Disease context

short stature due to GHSR deficiency — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Short stature due to GHSR deficiency (Orphanet):

Inheritance: Autosomal dominant, Autosomal recessive
Onset: Infancy, Neonatal

Similar variants

GHSR p.Arg141Pro Uncertain significance ★★ ⚠ same condition
GHSR p.Arg206Pro Uncertain significance ★★ ⚠ same condition
GHSR p.Arg237Trp Uncertain significance ★★ ⚠ same condition
GHSR p.Leu42Val Uncertain significance ★★ ⚠ same condition
GHSR p.Lys259Asn Uncertain significance ★★ ⚠ same condition
GHSR p.Ser252Leu Uncertain significance ★★ ⚠ same condition
GHSR c.*114A>G Benign ★★ same condition
GHSR c.*122C>T Benign ★★ same condition

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/ghsr-p-arg159 (accessed [today's date]).

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