Is FSHR p.Asn560fs (c.1679_1685del) pathogenic?

FSHR p.Asn560fs (c.16791685del) is classified Pathogenic in FSHR (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-10-01). Absent from gnomAD; Associated with Genetic non-acquired premature ovarian failure.

What condition is associated with FSHR p.Asn560fs (c.1679_1685del)?

FSHR p.Asn560fs (c.1679_1685del) is associated with Genetic non-acquired premature ovarian failure (ClinVar).

How common is FSHR p.Asn560fs (c.1679_1685del) in the general population?

FSHR p.Asn560fs (c.1679_1685del) is absent from gnomAD (gnomAD).

FSHR p.Asn560fs

c.1679_1685del · rs2103990623 · VCV1256040

Pathogenic No assertion criteria

Classification

Pathogenic

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

Genetic non-acquired premature ovarian failure

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function
NMD	escapes	premature termination codon in the last exon (10 of 10) — the truncated protein is likely expressed. PVS1 input, not an applied code
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP -0.34	GERP 0.47, phastCons 0.001

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: FSHR
Protein: p.Asn560fs
Coding: c.1679_1685del
MANE Select: NM_000145
dbSNP: rs2103990623
Type: Deletion
Location: chr2:48963136 (GRCh38)
Gene constraint: LOEUF 1.071 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 81.87 · 5 PDB
Residue 560: a turn

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

Disease context

Genetic non-acquired premature ovarian failure — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

FSHR p.Asn560= Likely benign ★ same residue
FSHR p.Gln117Ter Pathogenic same condition
FSHR p.Glu466Lys Likely pathogenic same condition
FSHR p.Ile588Thr Likely pathogenic same condition
FSHR p.Leu125Arg Likely pathogenic same condition
FSHR p.Ser295Phe Likely pathogenic ⚠ same condition
FSHR p.Thr228Ile Likely pathogenic same condition
FSHR p.Phe170fs Pathogenic/Likely pathogenic ★★ 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/fshr-p-asn560fs (accessed [today's date]).

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